Vegan-specific signature implies healthier metabolic profile: findings from diet-related multi-omics observational study based on different European populations
Statistical report for microbiome analysis
Authors and affiliations
Monika Cahova1,*, Anna Ouradova2,*, Giulio Ferrero3,4,*, Miriam Bratova1, Nikola Daskova1, Klara Dohnalova5, Marie Heczkova1, Karel Chalupsky5, Maria Kralova6,7, Marek Kuzma8, Filip Tichanek1, Lucie Najmanova8, Barbara Pardini10, Helena Pelantová8, Radislav Sedlacek5, Sonia Tarallo9, Petra Videnska10, Jan Gojda2,#, Alessio Naccarati9,#
* These authors have contributed equally to this work and share first authorship
# These authors have contributed equally to this work and share last authorship
1 Institute for Clinical and Experimental Medicine, Prague, Czech Republic
2 Department of Internal Medicine, Kralovske Vinohrady University Hospital and Third Faculty of Medicine, Charles University, Prague, Czech Republic 3 Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
4 Department of Computer Science, University of Turin, Turin, Italy
5 Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
6 Ambis University, Department of Economics and Management, Prague, Czech Republic
7 Department of Applied Mathematics and Computer Science, Masaryk University, Brno, Czech Republic
8 Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
9 Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
10 Mendel University, Department of Chemistry and Biochemistry, Brno, Czech Republic
This is a statistical report of the study Vegan-specific signature implies healthier metabolic profile: findings from diet-related multi-omics observational study based on different European populations that has been submitted to [TO BE ADDED]
When using this code or data, cite the original publication:
TO BE ADDED
BibTex citation for the original publication:
TO BE ADDED
Original GitHub repository: https://github.com/filip-tichanek/ItCzVegans
Statistical reports can be found on the reports hub.
Data analysis is described in detail in the statistical methods report.
1 Introduction
This project explores potential signatures of a vegan diet across the microbiome, metabolome, and lipidome. We used data from healthy vegan and omnivorous human subjects in two countries (Czech Republic and Italy), with subjects grouped by Country and Diet, resulting in four distinct groups.
To assess the generalizability of these findings, we validated our results with an independent cohort from the Czech Republic for external validation.
1.1 Statistical Methods
The statistical modeling approach is described in detail in this report. Briefly, the methods used included:
Multivariate analysis: We conducted multivariate analyses (PERMANOVA, PCA, correlation analyses) to explore the effects of
diet,country, and their possible interaction (diet : country) on the microbiome, lipidome, and metabolome compositions in an integrative manner. This part of the analysis is not available on the GitHub page, but the code will be provided upon request.Linear models: Linear models were applied to estimate the effects of
diet,country, and their interaction (diet:country) on individual lipids, metabolites, and bacterial taxa (“features”). Features that significantly differed between diet groups (based on the estimated average effect of diet across both countries, adjusted for multiple comparisons with FDR < 0.1) were further examined in the independent validation cohort to assess whether these associations were reproducible.Predictive models (elastic net): We employed elastic net (regularized) logistic regression to predict vegan status based on microbiome, metabolome, and lipidome features (one predictive model per dataset, i.e., three elastic net models in total). These models were internally validated using out-of-bag bootstrap resampling. The discriminatory power of each model to differentiate between diet groups was evaluated using the out-of-sample (optimism-corrected) area under the receiver operating characteristic curve (ROC-AUC). The models trained on the training data were then used to estimate the predicted probability that a given subject is vegan in an indepedent validation cohort. This predicted probability was subsequently used as a variable to discriminate between diet groups for external validation.
2 Initiation
2.1 Set home directory
Open code
setwd('/home/ticf/GitRepo/ticf/478_MOCA_italian')2.2 Upload initiation file
Open code
source('478_initiation.R')3 Data
3.1 Upload all original data
3.1.1 Training set
3.1.1.1 Connect metadata from lipidom table
Open code
training_metadata <- read.xlsx('gitignore/data/lipidome_training_cohort.xlsx') %>%
select(Sample, Country, Diet) %>%
mutate(ID = Sample)3.1.1.2 Connect italian data
Open code
data_microbiome_IT <- read.table(
'gitignore/data/0_Data_Metaphlan4_species_filtered_IT_rel_ab.txt') %>% t()
colnames(data_microbiome_IT) <- data_microbiome_IT[1,]
data_microbiome_IT <- data_microbiome_IT[-1,] %>% data.frame() %>%
mutate(
across(
Adlercreutzia_equolifaciens:Veillonella_atypica, ~ as.numeric(.)/100
)
) %>%
left_join(training_metadata, by = 'ID') %>%
select(Sample, Country, Diet, everything()) %>%
select(-ID)3.1.1.3 Connect czech data
Open code
data_microbiome_CZ <- read.table(
'gitignore/data/0_Data_Metaphlan4_species_filtered_Triema_rel_ab.txt') %>% t()
colnames(data_microbiome_CZ) <- data_microbiome_CZ[1,]
data_microbiome_CZ <- data_microbiome_CZ[-1,] %>% data.frame()
data_microbiome_CZ <- data_microbiome_CZ %>%
mutate(
across(
Adlercreutzia_equolifaciens:Veillonella_atypica, ~ as.numeric(.)/100
)
) %>%
left_join(training_metadata, by = 'ID') %>%
select(Sample, Country, Diet, everything()) %>%
select(-ID)3.1.1.4 Merging czech and italian data
Open code
data_microbiome_original_raw <- bind_rows(data_microbiome_CZ, data_microbiome_IT)
summary(data_microbiome_original_raw)
## Sample Country Diet
## Length:166 Length:166 Length:166
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
## Adlercreutzia_equolifaciens Agathobaculum_butyriciproducens
## Min. :0.000e+00 Min. :0.000000
## 1st Qu.:0.000e+00 1st Qu.:0.001169
## Median :3.445e-05 Median :0.002145
## Mean :2.322e-04 Mean :0.003461
## 3rd Qu.:1.853e-04 3rd Qu.:0.004470
## Max. :4.875e-03 Max. :0.025249
## Akkermansia_muciniphila Alistipes_communis Alistipes_finegoldii
## Min. :0.0000000 Min. :0.000000 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000241 1st Qu.:2.220e-06
## Median :0.0009167 Median :0.002489 Median :6.484e-04
## Mean :0.0114990 Mean :0.005551 Mean :3.641e-03
## 3rd Qu.:0.0089904 3rd Qu.:0.006985 3rd Qu.:3.530e-03
## Max. :0.2719445 Max. :0.062301 Max. :4.998e-02
## Alistipes_ihumii Alistipes_indistinctus Alistipes_onderdonkii
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0003857
## Median :0.0004706 Median :0.0000867 Median :0.0031382
## Mean :0.0023185 Mean :0.0007937 Mean :0.0145942
## 3rd Qu.:0.0025642 3rd Qu.:0.0006787 3rd Qu.:0.0122375
## Max. :0.0252111 Max. :0.0220987 Max. :0.1750433
## Alistipes_putredinis Alistipes_senegalensis Alistipes_shahii
## Min. :0.000000 Min. :0.000e+00 Min. :0.000000
## 1st Qu.:0.001969 1st Qu.:0.000e+00 1st Qu.:0.001151
## Median :0.020323 Median :5.500e-07 Median :0.005118
## Mean :0.031732 Mean :1.014e-03 Mean :0.009767
## 3rd Qu.:0.047024 3rd Qu.:8.605e-04 3rd Qu.:0.014467
## Max. :0.162515 Max. :4.685e-02 Max. :0.065784
## Anaerobutyricum_hallii Anaerofilum_hominis Anaeromassilibacillus_senegalensis
## Min. :0.000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000200 Median :0.000e+00 Median :4.750e-06
## Mean :0.001199 Mean :3.592e-05 Mean :9.213e-05
## 3rd Qu.:0.001499 3rd Qu.:1.245e-05 3rd Qu.:7.705e-05
## Max. :0.010241 Max. :1.020e-03 Max. :4.582e-03
## Anaerostipes_hadrus Anaerotignum_faecicola Anaerotruncus_colihominis
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:3.192e-05 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :8.779e-04 Median :0.0001417 Median :0.0000033
## Mean :4.366e-03 Mean :0.0016793 Mean :0.0001279
## 3rd Qu.:3.934e-03 3rd Qu.:0.0011429 3rd Qu.:0.0001127
## Max. :6.649e-02 Max. :0.0325208 Max. :0.0032344
## Anaerotruncus_massiliensis Anaerotruncus_rubiinfantis Bacteroides_caccae
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.000e+00 Median :1.350e-05 Median :0.0008121
## Mean :5.832e-05 Mean :5.911e-05 Mean :0.0036313
## 3rd Qu.:7.850e-06 3rd Qu.:8.100e-05 3rd Qu.:0.0035346
## Max. :1.608e-03 Max. :4.332e-04 Max. :0.0596008
## Bacteroides_cellulosilyticus Bacteroides_clarus Bacteroides_eggerthii
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.0000053 Median :0.0000000 Median :0.0000000
## Mean :0.0033031 Mean :0.0017244 Mean :0.0028440
## 3rd Qu.:0.0009843 3rd Qu.:0.0002202 3rd Qu.:0.0007432
## Max. :0.0949794 Max. :0.1004693 Max. :0.0553489
## Bacteroides_fragilis Bacteroides_ovatus Bacteroides_stercoris
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0003829 1st Qu.:0.0000000
## Median :0.0000000 Median :0.0018786 Median :0.0000088
## Mean :0.0013740 Mean :0.0087568 Mean :0.0110969
## 3rd Qu.:0.0002518 3rd Qu.:0.0080833 3rd Qu.:0.0044142
## Max. :0.0527658 Max. :0.1835700 Max. :0.1933994
## Bacteroides_thetaiotaomicron Bacteroides_uniformis Bacteroides_xylanisolvens
## Min. :0.000e+00 Min. :0.00000 Min. :0.000e+00
## 1st Qu.:2.998e-05 1st Qu.:0.00478 1st Qu.:1.432e-05
## Median :5.684e-04 Median :0.01814 Median :1.836e-04
## Mean :2.592e-03 Mean :0.03531 Mean :2.843e-03
## 3rd Qu.:2.370e-03 3rd Qu.:0.04496 3rd Qu.:1.746e-03
## Max. :4.940e-02 Max. :0.20757 Max. :1.622e-01
## Barnesiella_intestinihominis Bifidobacterium_adolescentis
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:5.347e-05 1st Qu.:3.222e-05
## Median :1.172e-03 Median :2.265e-03
## Mean :3.144e-03 Mean :6.628e-03
## 3rd Qu.:3.539e-03 3rd Qu.:8.386e-03
## Max. :2.845e-02 Max. :7.717e-02
## Bifidobacterium_longum Bilophila_SGB15451 Bilophila_wadsworthia
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0003053 1st Qu.:0.0000000 1st Qu.:0.0001018
## Median :0.0016524 Median :0.0000000 Median :0.0005542
## Mean :0.0059831 Mean :0.0001598 Mean :0.0015594
## 3rd Qu.:0.0040142 3rd Qu.:0.0000000 3rd Qu.:0.0018417
## Max. :0.1582122 Max. :0.0048426 Max. :0.0194645
## Blautia_faecis Blautia_glucerasea Blautia_massiliensis
## Min. :0.0000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.0000874 1st Qu.:9.875e-06 1st Qu.:0.0000000
## Median :0.0004041 Median :1.647e-04 Median :0.0001212
## Mean :0.0013417 Mean :4.602e-04 Mean :0.0018358
## 3rd Qu.:0.0013706 3rd Qu.:5.990e-04 3rd Qu.:0.0013415
## Max. :0.0327014 Max. :5.534e-03 Max. :0.0664897
## Blautia_obeum Blautia_sp_MCC283 Blautia_wexlerae
## Min. :0.0000000 Min. :0.000e+00 Min. :0.000000
## 1st Qu.:0.0000492 1st Qu.:0.000e+00 1st Qu.:0.000149
## Median :0.0002816 Median :9.185e-05 Median :0.001101
## Mean :0.0010843 Mean :1.117e-03 Mean :0.005289
## 3rd Qu.:0.0011403 3rd Qu.:6.552e-04 3rd Qu.:0.004533
## Max. :0.0230052 Max. :7.301e-02 Max. :0.117828
## Brotolimicola_acetigignens Butyricimonas_faecihominis Butyricimonas_virosa
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0002889 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.0010865 Median :0.0000000 Median :0.0000000
## Mean :0.0065503 Mean :0.0002135 Mean :0.0001199
## 3rd Qu.:0.0043654 3rd Qu.:0.0001897 3rd Qu.:0.0000636
## Max. :0.1078520 Max. :0.0046050 Max. :0.0038677
## Candidatus_Borkfalkia_ceftriaxoniphila Candidatus_Cibionibacter_quicibialis
## Min. :0.000e+00 Min. :0.000000
## 1st Qu.:0.000e+00 1st Qu.:0.002497
## Median :0.000e+00 Median :0.008757
## Mean :2.061e-04 Mean :0.016591
## 3rd Qu.:2.572e-05 3rd Qu.:0.018056
## Max. :5.555e-03 Max. :0.160329
## Clostridia_bacterium_UC5_1_1D1 Clostridiaceae_bacterium
## Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0001688
## Median :9.200e-06 Median :0.0009697
## Mean :6.736e-05 Mean :0.0027794
## 3rd Qu.:5.440e-05 3rd Qu.:0.0033770
## Max. :1.829e-03 Max. :0.0288186
## Clostridiaceae_bacterium_AF18_31LB Clostridiaceae_bacterium_Marseille_Q4143
## Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000653 1st Qu.:5.650e-06
## Median :0.0002154 Median :6.825e-05
## Mean :0.0005095 Mean :1.843e-04
## 3rd Qu.:0.0005462 3rd Qu.:2.342e-04
## Max. :0.0083933 Max. :1.895e-03
## Clostridiaceae_bacterium_Marseille_Q4145 Clostridiales_bacterium
## Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000266
## Median :1.720e-05 Median :0.0002925
## Mean :6.544e-05 Mean :0.0010598
## 3rd Qu.:7.700e-05 3rd Qu.:0.0011261
## Max. :8.947e-04 Max. :0.0299120
## Clostridiales_bacterium_KLE1615 Clostridium_SGB4750 Clostridium_SGB4909
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:5.265e-05 1st Qu.:7.420e-06 1st Qu.:0.0000000
## Median :5.064e-04 Median :8.570e-05 Median :0.0000000
## Mean :1.227e-03 Mean :1.011e-03 Mean :0.0008375
## 3rd Qu.:1.685e-03 3rd Qu.:6.413e-04 3rd Qu.:0.0001642
## Max. :1.037e-02 Max. :4.993e-02 Max. :0.0359632
## Clostridium_fessum Clostridium_leptum Clostridium_sp_AF20_17LB
## Min. :0.0000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.0005066 1st Qu.:0.000e+00 1st Qu.:2.498e-05
## Median :0.0015853 Median :3.415e-05 Median :2.959e-04
## Mean :0.0035494 Mean :4.016e-04 Mean :8.341e-04
## 3rd Qu.:0.0040255 3rd Qu.:1.088e-04 3rd Qu.:1.096e-03
## Max. :0.0510927 Max. :3.291e-02 Max. :7.102e-03
## Clostridium_sp_AF27_2AA Clostridium_sp_AF36_4 Clostridium_sp_AM22_11AC
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0001011
## Median :0.0001306 Median :0.0001521 Median :0.0005213
## Mean :0.0007414 Mean :0.0022566 Mean :0.0021444
## 3rd Qu.:0.0004987 3rd Qu.:0.0014196 3rd Qu.:0.0021354
## Max. :0.0175781 Max. :0.0835989 Max. :0.0263489
## Clostridium_sp_AM33_3 Collinsella_aerofaciens Coprobacter_fastidiosus
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:6.235e-05 1st Qu.:0.0002452 1st Qu.:0.0000000
## Median :3.146e-04 Median :0.0008033 Median :0.0000000
## Mean :8.151e-04 Mean :0.0017892 Mean :0.0002232
## 3rd Qu.:7.753e-04 3rd Qu.:0.0022898 3rd Qu.:0.0001505
## Max. :1.569e-02 Max. :0.0235808 Max. :0.0065932
## Coprococcus_catus Coprococcus_comes Coprococcus_eutactus
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:2.735e-05 1st Qu.:1.875e-05 1st Qu.:0.0000000
## Median :3.185e-04 Median :2.600e-04 Median :0.0007131
## Mean :5.147e-04 Mean :9.327e-04 Mean :0.0052089
## 3rd Qu.:6.389e-04 3rd Qu.:8.071e-04 3rd Qu.:0.0052116
## Max. :5.175e-03 Max. :1.307e-02 Max. :0.1018948
## Dorea_formicigenerans Dorea_longicatena Dorea_sp_AF36_15AT
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:6.925e-06 1st Qu.:4.225e-05 1st Qu.:0.0000000
## Median :1.640e-04 Median :5.707e-04 Median :0.0000212
## Mean :4.927e-04 Mean :1.745e-03 Mean :0.0001276
## 3rd Qu.:6.154e-04 3rd Qu.:2.034e-03 3rd Qu.:0.0001202
## Max. :5.509e-03 Max. :3.282e-02 Max. :0.0018086
## Dysosmobacter_SGB15077 Dysosmobacter_welbionis Eggerthella_lenta
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.0002946 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.0010386 Median :0.000e+00
## Mean :3.268e-04 Mean :0.0029821 Mean :1.296e-04
## 3rd Qu.:1.722e-05 3rd Qu.:0.0040171 3rd Qu.:3.222e-05
## Max. :1.258e-02 Max. :0.0421230 Max. :5.440e-03
## Enterocloster_citroniae Enterocloster_hominis Escherichia_coli
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.0000150 Median :0.0000000 Median :0.0001308
## Mean :0.0001126 Mean :0.0005085 Mean :0.0013753
## 3rd Qu.:0.0000869 3rd Qu.:0.0001440 3rd Qu.:0.0006760
## Max. :0.0021971 Max. :0.0111120 Max. :0.0522880
## Eubacterium_ramulus Eubacterium_rectale Eubacterium_siraeum
## Min. :0.0000000 Min. :0.000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.001165 1st Qu.:0.0000000
## Median :0.0000805 Median :0.005220 Median :0.0000000
## Mean :0.0002872 Mean :0.014922 Mean :0.0012085
## 3rd Qu.:0.0002941 3rd Qu.:0.016470 3rd Qu.:0.0002872
## Max. :0.0034632 Max. :0.109626 Max. :0.0352094
## Eubacterium_ventriosum Faecalibacterium_SGB15346 Faecalibacterium_prausnitzii
## Min. :0.000e+00 Min. :0.0000000 Min. :0.00000
## 1st Qu.:0.000e+00 1st Qu.:0.0005724 1st Qu.:0.02017
## Median :6.945e-05 Median :0.0029065 Median :0.04250
## Mean :8.707e-04 Mean :0.0063215 Mean :0.05886
## 3rd Qu.:5.903e-04 3rd Qu.:0.0085679 3rd Qu.:0.08075
## Max. :2.029e-02 Max. :0.0799532 Max. :0.33216
## Faecalibacterium_sp_CLA_AA_H233 Faecalibacterium_sp_HTFF
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:4.850e-06 1st Qu.:0.000e+00
## Median :2.348e-04 Median :7.785e-05
## Mean :2.630e-03 Mean :1.182e-03
## 3rd Qu.:1.499e-03 3rd Qu.:1.062e-03
## Max. :5.355e-02 Max. :2.208e-02
## Faecalicatena_fissicatena Flavonifractor_plautii
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:1.585e-05 1st Qu.:3.105e-05
## Median :3.200e-04 Median :2.823e-04
## Mean :1.050e-03 Mean :1.355e-03
## 3rd Qu.:1.174e-03 3rd Qu.:1.116e-03
## Max. :1.405e-02 Max. :2.862e-02
## Fusicatenibacter_saccharivorans Fusicatenibacter_sp_CLA_AA_H277
## Min. :0.000000 Min. :0.000e+00
## 1st Qu.:0.001050 1st Qu.:5.675e-05
## Median :0.002624 Median :2.263e-04
## Mean :0.004965 Mean :4.027e-04
## 3rd Qu.:0.005350 3rd Qu.:5.232e-04
## Max. :0.061662 Max. :4.875e-03
## GGB13404_SGB14252 GGB1420_SGB1957 GGB2653_SGB3574
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :3.350e-06 Median :0.0000000 Median :0.0000241
## Mean :1.583e-04 Mean :0.0003116 Mean :0.0001354
## 3rd Qu.:1.745e-04 3rd Qu.:0.0000000 3rd Qu.:0.0001323
## Max. :2.198e-03 Max. :0.0079631 Max. :0.0044801
## GGB2998_SGB3988 GGB3034_SGB4030 GGB3109_SGB4121
## Min. :0.0000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.0000000 Median :0.000e+00 Median :8.050e-06
## Mean :0.0001071 Mean :1.096e-05 Mean :4.249e-04
## 3rd Qu.:0.0000801 3rd Qu.:0.000e+00 3rd Qu.:3.460e-04
## Max. :0.0025680 Max. :2.346e-04 Max. :6.376e-03
## GGB3175_SGB4191 GGB33469_SGB15236 GGB33512_SGB15203
## Min. :0.0000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.0000000 Median :3.005e-05 Median :0.000e+00
## Mean :0.0028154 Mean :1.712e-03 Mean :7.039e-04
## 3rd Qu.:0.0004661 3rd Qu.:1.273e-03 3rd Qu.:5.617e-05
## Max. :0.0515210 Max. :4.202e-02 Max. :4.454e-02
## GGB33586_SGB53517 GGB3537_SGB4727 GGB38744_SGB14842
## Min. :0.0000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.0000000 Median :0.000e+00 Median :0.000e+00
## Mean :0.0002087 Mean :3.764e-05 Mean :5.670e-06
## 3rd Qu.:0.0001938 3rd Qu.:1.915e-05 3rd Qu.:0.000e+00
## Max. :0.0039798 Max. :1.368e-03 Max. :1.931e-04
## GGB45432_SGB63101 GGB45613_SGB63326 GGB47687_SGB2286
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :3.050e-06 Median :0.000e+00 Median :0.0000000
## Mean :3.901e-05 Mean :1.626e-05 Mean :0.0028797
## 3rd Qu.:4.275e-05 3rd Qu.:1.217e-05 3rd Qu.:0.0007292
## Max. :8.899e-04 Max. :7.168e-04 Max. :0.1126518
## GGB52106_SGB72838 GGB52130_SGB14966 GGB9062_SGB13981
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.000e+00 Median :7.395e-05 Median :0.0000000
## Mean :3.494e-05 Mean :1.876e-04 Mean :0.0001584
## 3rd Qu.:1.155e-05 3rd Qu.:2.760e-04 3rd Qu.:0.0000683
## Max. :9.622e-04 Max. :2.031e-03 Max. :0.0022193
## GGB9063_SGB13982 GGB9064_SGB13983 GGB9342_SGB14306 GGB9345_SGB14311
## Min. :0.0000000 Min. :0.0000000 Min. :0.000e+00 Min. :0.000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.000000
## Median :0.0000000 Median :0.0000000 Median :7.350e-06 Median :0.000000
## Mean :0.0003579 Mean :0.0004445 Mean :1.645e-03 Mean :0.001554
## 3rd Qu.:0.0001142 3rd Qu.:0.0001410 3rd Qu.:7.287e-04 3rd Qu.:0.000609
## Max. :0.0179030 Max. :0.0136173 Max. :3.655e-02 Max. :0.030108
## GGB9453_SGB14844 GGB9502_SGB14899 GGB9509_SGB14906
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.0000000 Median :0.0000000 Median :0.0000000
## Mean :0.0001438 Mean :0.0002479 Mean :0.0005623
## 3rd Qu.:0.0000136 3rd Qu.:0.0003216 3rd Qu.:0.0002062
## Max. :0.0160739 Max. :0.0053168 Max. :0.0298472
## GGB9522_SGB14921 GGB9531_SGB14932 GGB9534_SGB14937 GGB9602_SGB15031
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000 Min. :0.000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.000000
## Median :0.000e+00 Median :0.000e+00 Median :0.0000369 Median :0.000073
## Mean :8.645e-05 Mean :8.689e-05 Mean :0.0003241 Mean :0.002779
## 3rd Qu.:6.947e-05 3rd Qu.:5.728e-05 3rd Qu.:0.0002522 3rd Qu.:0.001375
## Max. :2.344e-03 Max. :1.621e-03 Max. :0.0118852 Max. :0.057453
## GGB9614_SGB15049 GGB9619_SGB15067 GGB9621_SGB15073
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:2.925e-06 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :3.113e-04 Median :0.0000000 Median :0.0000000
## Mean :1.012e-03 Mean :0.0001688 Mean :0.0003440
## 3rd Qu.:1.303e-03 3rd Qu.:0.0001388 3rd Qu.:0.0004201
## Max. :9.384e-03 Max. :0.0028069 Max. :0.0026832
## GGB9635_SGB15106 GGB9646_SGB15123 GGB9667_SGB15164
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :2.305e-05 Median :0.0000103 Median :0.0000159
## Mean :1.074e-02 Mean :0.0001020 Mean :0.0004053
## 3rd Qu.:5.986e-03 3rd Qu.:0.0001008 3rd Qu.:0.0003939
## Max. :1.383e-01 Max. :0.0018468 Max. :0.0042443
## GGB9699_SGB15216 GGB9708_SGB15234 GGB9715_SGB15265
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:4.528e-05 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :3.890e-04 Median :0.0001936 Median :0.0002471
## Mean :1.259e-03 Mean :0.0037159 Mean :0.0070566
## 3rd Qu.:1.726e-03 3rd Qu.:0.0022052 3rd Qu.:0.0063499
## Max. :1.577e-02 Max. :0.0882956 Max. :0.1487586
## GGB9719_SGB15272 GGB9719_SGB15273 GGB9730_SGB15291 GGB9758_SGB15368
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000 Min. :0.000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0000550 1st Qu.:0.000000
## Median :0.0000000 Median :0.0000000 Median :0.0005648 Median :0.001519
## Mean :0.0001319 Mean :0.0000583 Mean :0.0011109 Mean :0.019032
## 3rd Qu.:0.0001295 3rd Qu.:0.0000015 3rd Qu.:0.0012614 3rd Qu.:0.022600
## Max. :0.0029524 Max. :0.0019590 Max. :0.0122176 Max. :0.290886
## GGB9760_SGB15373 GGB9765_SGB15382 GGB9770_SGB15390
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:3.035e-05 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :3.542e-04 Median :0.000e+00 Median :0.000e+00
## Mean :8.777e-04 Mean :6.240e-05 Mean :1.359e-04
## 3rd Qu.:9.922e-04 3rd Qu.:1.657e-05 3rd Qu.:5.283e-05
## Max. :1.301e-02 Max. :1.829e-03 Max. :4.034e-03
## GGB9775_SGB15395 GGB9781_SGB15402 GGB9818_SGB15459
## Min. :0.0000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.0000000 Median :0.000e+00 Median :0.0000000
## Mean :0.0002453 Mean :1.531e-05 Mean :0.0003090
## 3rd Qu.:0.0000375 3rd Qu.:2.450e-06 3rd Qu.:0.0001238
## Max. :0.0061360 Max. :4.557e-04 Max. :0.0072002
## Gemmiger_formicilis Guopingia_tenuis Holdemania_filiformis
## Min. :0.000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.001873 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.005235 Median :0.000e+00 Median :2.950e-06
## Mean :0.010605 Mean :2.629e-05 Mean :1.214e-04
## 3rd Qu.:0.013073 3rd Qu.:3.280e-05 3rd Qu.:8.608e-05
## Max. :0.124274 Max. :4.077e-04 Max. :1.739e-03
## Hydrogenoanaerobacterium_saccharovorans Intestinimonas_butyriciproducens
## Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.0004149 Median :0.0000497
## Mean :0.0008410 Mean :0.0003672
## 3rd Qu.:0.0012499 3rd Qu.:0.0002387
## Max. :0.0068933 Max. :0.0076464
## Intestinimonas_gabonensis Intestinimonas_massiliensis
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :3.350e-05 Median :0.000e+00
## Mean :7.254e-05 Mean :2.710e-04
## 3rd Qu.:1.120e-04 3rd Qu.:9.995e-05
## Max. :5.578e-04 Max. :5.890e-03
## Lachnoclostridium_sp_An138 Lachnospira_eligens Lachnospira_pectinoschiza
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000837 1st Qu.:0.0004423
## Median :0.000e+00 Median :0.0010730 Median :0.0024533
## Mean :1.229e-05 Mean :0.0060395 Mean :0.0105211
## 3rd Qu.:0.000e+00 3rd Qu.:0.0060136 3rd Qu.:0.0108216
## Max. :4.719e-04 Max. :0.0711575 Max. :0.1491405
## Lachnospiraceae_bacterium Lachnospiraceae_bacterium_AM48_27BH
## Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:5.312e-05 1st Qu.:0.0000058
## Median :3.161e-04 Median :0.0001449
## Mean :1.499e-03 Mean :0.0004808
## 3rd Qu.:1.252e-03 3rd Qu.:0.0007510
## Max. :2.828e-02 Max. :0.0036770
## Lachnospiraceae_bacterium_CLA_AA_H215 Lachnospiraceae_bacterium_CLA_AA_H244
## Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0003953
## Median :0.0000196 Median :0.0011186
## Mean :0.0001348 Mean :0.0030128
## 3rd Qu.:0.0001249 3rd Qu.:0.0027737
## Max. :0.0017039 Max. :0.0417129
## Lachnotalea_sp_AF33_28 Lacrimispora_amygdalina Lawsonibacter_SGB15145
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0001620 1st Qu.:0.0000000
## Median :0.000e+00 Median :0.0006867 Median :0.0000432
## Mean :2.355e-05 Mean :0.0015083 Mean :0.0003115
## 3rd Qu.:1.962e-05 3rd Qu.:0.0018513 3rd Qu.:0.0003499
## Max. :5.779e-04 Max. :0.0157674 Max. :0.0043012
## Lawsonibacter_asaccharolyticus Lawsonibacter_hominis Ligaoa_zhengdingensis
## Min. :0.0000000 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000846 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.0004759 Median :0.0000097 Median :0.000e+00
## Mean :0.0019247 Mean :0.0002159 Mean :2.402e-05
## 3rd Qu.:0.0021256 3rd Qu.:0.0001272 3rd Qu.:1.962e-05
## Max. :0.0304000 Max. :0.0053049 Max. :2.281e-04
## Mediterraneibacter_faecis Odoribacter_splanchnicus Oliverpabstia_intestinalis
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0001976 1st Qu.:0.0000000
## Median :5.955e-05 Median :0.0007932 Median :0.0000556
## Mean :7.432e-04 Mean :0.0015979 Mean :0.0006646
## 3rd Qu.:5.370e-04 3rd Qu.:0.0022577 3rd Qu.:0.0005179
## Max. :1.094e-02 Max. :0.0104102 Max. :0.0164907
## Oscillibacter_sp_ER4 Oscillibacter_sp_MSJ_31 Oscillibacter_sp_PC13
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:4.378e-05 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :4.039e-03 Median :0.0009371 Median :0.000e+00
## Mean :9.269e-03 Mean :0.0061000 Mean :2.549e-05
## 3rd Qu.:1.198e-02 3rd Qu.:0.0059364 3rd Qu.:3.142e-05
## Max. :6.875e-02 Max. :0.1408486 Max. :2.627e-04
## Oscillibacter_valericigenes Oscillospiraceae_bacterium
## Min. :0.0000000 Min. :0.000000
## 1st Qu.:0.0005627 1st Qu.:0.000000
## Median :0.0016343 Median :0.000192
## Mean :0.0037479 Mean :0.002295
## 3rd Qu.:0.0045934 3rd Qu.:0.001233
## Max. :0.0462371 Max. :0.094657
## Oscillospiraceae_bacterium_CLA_AA_H250
## Min. :0.000e+00
## 1st Qu.:3.502e-05
## Median :4.721e-04
## Mean :1.267e-03
## 3rd Qu.:1.347e-03
## Max. :2.662e-02
## Oscillospiraceae_bacterium_Marseille_Q3528 Parabacteroides_distasonis
## Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0005998
## Median :0.0001102 Median :0.0021084
## Mean :0.0002187 Mean :0.0040434
## 3rd Qu.:0.0002662 3rd Qu.:0.0055781
## Max. :0.0029340 Max. :0.0319649
## Parabacteroides_merdae Paraprevotella_clara Parasutterella_excrementihominis
## Min. :0.000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.001745 Median :1.005e-05 Median :0.0000925
## Mean :0.004220 Mean :3.847e-03 Mean :0.0016349
## 3rd Qu.:0.005745 3rd Qu.:5.190e-03 3rd Qu.:0.0007551
## Max. :0.042251 Max. :6.890e-02 Max. :0.0317369
## Phascolarctobacterium_faecium Phocaeicola_dorei Phocaeicola_sartorii
## Min. :0.000000 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000000 1st Qu.:0.0000012 1st Qu.:0.000e+00
## Median :0.000000 Median :0.0007404 Median :0.000e+00
## Mean :0.005069 Mean :0.0108577 Mean :5.930e-06
## 3rd Qu.:0.001155 3rd Qu.:0.0092181 3rd Qu.:1.575e-06
## Max. :0.143305 Max. :0.1978448 Max. :8.170e-05
## Phocaeicola_vulgatus Phocea_massiliensis Provencibacterium_massiliense
## Min. :0.000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.002865 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.011614 Median :0.000e+00 Median :0.000e+00
## Mean :0.035908 Mean :7.498e-05 Mean :1.407e-05
## 3rd Qu.:0.038286 3rd Qu.:8.520e-05 3rd Qu.:8.925e-06
## Max. :0.307894 Max. :1.255e-03 Max. :2.829e-04
## Pseudoflavonifractor_capillosus Roseburia_faecis Roseburia_hominis
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:6.042e-05 1st Qu.:0.0002858
## Median :1.700e-06 Median :1.138e-03 Median :0.0013928
## Mean :2.400e-04 Mean :7.160e-03 Mean :0.0040151
## 3rd Qu.:9.677e-05 3rd Qu.:5.784e-03 3rd Qu.:0.0042910
## Max. :1.109e-02 Max. :2.296e-01 Max. :0.0796848
## Roseburia_intestinalis Roseburia_inulinivorans Ruminococcus_bicirculans
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0002055 1st Qu.:0.0000348
## Median :0.0000717 Median :0.0009830 Median :0.0007192
## Mean :0.0021826 Mean :0.0039152 Mean :0.0029495
## 3rd Qu.:0.0011131 3rd Qu.:0.0034006 3rd Qu.:0.0033711
## Max. :0.0499108 Max. :0.0620626 Max. :0.0270153
## Ruminococcus_bromii Ruminococcus_torques Ruthenibacterium_lactatiformans
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0001935
## Median :0.0008906 Median :0.0000008 Median :0.0005254
## Mean :0.0070197 Mean :0.0005111 Mean :0.0014620
## 3rd Qu.:0.0050637 3rd Qu.:0.0002775 3rd Qu.:0.0015064
## Max. :0.1629682 Max. :0.0149266 Max. :0.0358279
## Segatella_copri Simiaoa_sunii Streptococcus_salivarius
## Min. :0.000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000000 1st Qu.:4.175e-05 1st Qu.:0.0000000
## Median :0.000000 Median :3.548e-04 Median :0.0000425
## Mean :0.053750 Mean :5.804e-03 Mean :0.0002862
## 3rd Qu.:0.002339 3rd Qu.:1.894e-03 3rd Qu.:0.0002217
## Max. :0.875153 Max. :1.305e-01 Max. :0.0060953
## Streptococcus_thermophilus Sutterella_wadsworthensis Vescimonas_coprocola
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:5.225e-05
## Median :0.000e+00 Median :0.0005466 Median :3.524e-04
## Mean :4.705e-04 Mean :0.0080873 Mean :1.540e-03
## 3rd Qu.:8.098e-05 3rd Qu.:0.0078811 3rd Qu.:1.695e-03
## Max. :1.331e-02 Max. :0.1077498 Max. :1.477e-02
## Wansuia_hejianensis Youxingia_wuxianensis bacterium_210917_DFI_7_65
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.000e+00 Median :4.355e-05
## Mean :8.419e-06 Mean :1.314e-05 Mean :1.739e-04
## 3rd Qu.:4.950e-06 3rd Qu.:1.177e-05 3rd Qu.:2.004e-04
## Max. :9.910e-05 Max. :3.276e-04 Max. :2.070e-03
## Bacteroides_faecis Clostridiaceae_unclassified_SGB4771
## Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.0000000 Median :2.550e-06
## Mean :0.0016892 Mean :2.457e-04
## 3rd Qu.:0.0003732 3rd Qu.:2.629e-04
## Max. :0.0924332 Max. :7.316e-03
## Clostridium_sp_AM49_4BH Colidextribacter_sp_210702_DFI_3_9
## Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.0000186 Median :0.000e+00
## Mean :0.0009479 Mean :7.751e-05
## 3rd Qu.:0.0006711 3rd Qu.:8.565e-05
## Max. :0.0137412 Max. :2.295e-03
## Enterocloster_lavalensis GGB2982_SGB3964 GGB3304_SGB4367
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.000000
## Median :0.000e+00 Median :0.0000000 Median :0.000000
## Mean :3.657e-05 Mean :0.0001603 Mean :0.006249
## 3rd Qu.:1.895e-05 3rd Qu.:0.0000758 3rd Qu.:0.004215
## Max. :7.739e-04 Max. :0.0062970 Max. :0.074871
## GGB3619_SGB4894 GGB9296_SGB14253 GGB9524_SGB14924
## Min. :0.0000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.0000000 Median :0.000e+00 Median :0.0000000
## Mean :0.0004313 Mean :1.571e-04 Mean :0.0003030
## 3rd Qu.:0.0000683 3rd Qu.:6.025e-05 3rd Qu.:0.0001647
## Max. :0.0159758 Max. :3.502e-03 Max. :0.0143200
## GGB9574_SGB14987 GGB9619_SGB15066 GGB9707_SGB15229
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.000e+00 Median :0.000e+00 Median :0.0002587
## Mean :3.523e-05 Mean :9.250e-05 Mean :0.0009222
## 3rd Qu.:1.410e-05 3rd Qu.:4.750e-07 3rd Qu.:0.0010870
## Max. :7.737e-04 Max. :2.504e-03 Max. :0.0138493
## GGB9708_SGB15233 GGB9760_SGB15374 Roseburia_sp_AF02_12
## Min. :0.0000000 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.0000000 Median :0.0000000 Median :0.0000331
## Mean :0.0012046 Mean :0.0005325 Mean :0.0011198
## 3rd Qu.:0.0003848 3rd Qu.:0.0005236 3rd Qu.:0.0004146
## Max. :0.0814039 Max. :0.0080872 Max. :0.0369606
## Segatella_brunsvicensis Wujia_chipingensis Alistipes_dispar
## Min. :0.00000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.00000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.00000 Median :1.350e-06 Median :0.0000000
## Mean :0.01194 Mean :3.619e-03 Mean :0.0006519
## 3rd Qu.:0.00000 3rd Qu.:1.596e-03 3rd Qu.:0.0002937
## Max. :0.49458 Max. :5.839e-02 Max. :0.0180946
## Alistipes_sp_AF17_16 Anaerobutyricum_soehngenii Anaerosacchariphilus_sp_NSJ_68
## Min. :0.000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000000 Median :0.000e+00 Median :0.000e+00
## Mean :0.000748 Mean :2.674e-04 Mean :2.093e-05
## 3rd Qu.:0.000610 3rd Qu.:5.907e-05 3rd Qu.:2.445e-05
## Max. :0.025402 Max. :1.237e-02 Max. :4.210e-04
## Anaerotignum_sp_MSJ_24 Bittarella_massiliensis Blautia_SGB4815
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.000e+00 Median :1.865e-05
## Mean :7.179e-05 Mean :5.698e-06 Mean :1.717e-04
## 3rd Qu.:4.945e-05 3rd Qu.:0.000e+00 3rd Qu.:1.663e-04
## Max. :1.074e-03 Max. :1.359e-04 Max. :2.406e-03
## Blautia_luti Blautia_sp_OF03_15BH Butyricimonas_paravirosa
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :2.500e-07 Median :0.000e+00 Median :0.000e+00
## Mean :2.047e-04 Mean :2.752e-05 Mean :1.116e-04
## 3rd Qu.:1.812e-04 3rd Qu.:7.575e-06 3rd Qu.:4.282e-05
## Max. :3.159e-03 Max. :5.829e-04 Max. :2.880e-03
## Catenibacillus_scindens Clostridiaceae_bacterium_Marseille_Q4149
## Min. :0.000e+00 Min. :0.000000
## 1st Qu.:0.000e+00 1st Qu.:0.000000
## Median :0.000e+00 Median :0.000000
## Mean :2.672e-06 Mean :0.002353
## 3rd Qu.:0.000e+00 3rd Qu.:0.000518
## Max. :1.314e-04 Max. :0.071946
## Clostridium_SGB6173 Clostridium_SGB6179 Clostridium_sp_Marseille_P3244
## Min. :0.0000000 Min. :0.000e+00 Min. :0.00e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.00e+00
## Median :0.0000000 Median :0.000e+00 Median :0.00e+00
## Mean :0.0002150 Mean :2.551e-04 Mean :1.64e-06
## 3rd Qu.:0.0000594 3rd Qu.:1.477e-05 3rd Qu.:0.00e+00
## Max. :0.0070830 Max. :1.128e-02 Max. :4.92e-05
## Clostridium_sp_NSJ_42 Coprobacter_secundus Eubacteriaceae_bacterium
## Min. :0.0000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.0000000 Median :0.000e+00 Median :0.0000069
## Mean :0.0002742 Mean :5.297e-05 Mean :0.0009817
## 3rd Qu.:0.0000000 3rd Qu.:2.170e-05 3rd Qu.:0.0001183
## Max. :0.0242940 Max. :1.561e-03 Max. :0.0525183
## Faecalibacillus_faecis Faecalibacillus_intestinalis GGB13489_SGB15224
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.0000000
## Median :0.000e+00 Median :0.0001854 Median :0.0000000
## Mean :1.902e-04 Mean :0.0010312 Mean :0.0004354
## 3rd Qu.:7.625e-06 3rd Qu.:0.0011422 3rd Qu.:0.0004191
## Max. :6.796e-03 Max. :0.0196735 Max. :0.0052515
## GGB2970_SGB3952 GGB3352_SGB4436 GGB34797_SGB14322
## Min. :0.0000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.0000000 Median :0.000e+00 Median :0.0000000
## Mean :0.0001193 Mean :1.587e-05 Mean :0.0002539
## 3rd Qu.:0.0000663 3rd Qu.:0.000e+00 3rd Qu.:0.0001889
## Max. :0.0017474 Max. :4.009e-04 Max. :0.0054767
## GGB34900_SGB14891 GGB3653_SGB4964 GGB4456_SGB6141
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.0000007 Median :0.000e+00
## Mean :8.752e-06 Mean :0.0005639 Mean :5.739e-05
## 3rd Qu.:0.000e+00 3rd Qu.:0.0004370 3rd Qu.:0.000e+00
## Max. :1.698e-04 Max. :0.0092754 Max. :1.605e-03
## GGB4552_SGB6276 GGB51441_SGB71759 GGB58158_SGB79798
## Min. :0.0000000 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.0000000 Median :0.0000190 Median :0.000e+00
## Mean :0.0016796 Mean :0.0001130 Mean :6.287e-06
## 3rd Qu.:0.0005256 3rd Qu.:0.0001015 3rd Qu.:2.700e-06
## Max. :0.0681626 Max. :0.0023149 Max. :2.230e-04
## GGB9365_SGB14341 GGB9412_SGB14770 GGB9627_SGB15081 GGB9712_SGB15244
## Min. :0.000e+00 Min. :0.0000000 Min. :0.0000000 Min. :0.000000
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.000000
## Median :0.000e+00 Median :0.0000000 Median :0.0000375 Median :0.000000
## Mean :1.912e-04 Mean :0.0002044 Mean :0.0008485 Mean :0.000957
## 3rd Qu.:6.583e-05 3rd Qu.:0.0000000 3rd Qu.:0.0008041 3rd Qu.:0.000137
## Max. :4.736e-03 Max. :0.0091035 Max. :0.0086268 Max. :0.017285
## GGB9747_SGB15356 GGB9767_SGB15385 GGB9787_SGB15410 GGB9790_SGB15413
## Min. :0.000000 Min. :0.000e+00 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000000 Median :0.000e+00 Median :0.000e+00 Median :0.000e+00
## Mean :0.002757 Mean :1.957e-04 Mean :4.775e-05 Mean :4.165e-05
## 3rd Qu.:0.001799 3rd Qu.:6.407e-05 3rd Qu.:2.465e-05 3rd Qu.:0.000e+00
## Max. :0.038223 Max. :5.067e-03 Max. :7.156e-04 Max. :6.338e-04
## Haemophilus_parainfluenzae Intestinibacter_bartlettii Lachnospira_sp_NSJ_43
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.0000000 Median :3.465e-05
## Mean :7.688e-05 Mean :0.0001579 Mean :2.091e-03
## 3rd Qu.:6.148e-05 3rd Qu.:0.0000672 3rd Qu.:1.183e-03
## Max. :1.461e-03 Max. :0.0022551 Max. :6.286e-02
## Lachnospiraceae_bacterium_OM04_12BH Lactococcus_lactis
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.000e+00
## Mean :1.669e-04 Mean :9.802e-05
## 3rd Qu.:4.278e-05 3rd Qu.:0.000e+00
## Max. :6.780e-03 Max. :6.193e-03
## Lentihominibacter_faecis Massilioclostridium_coli
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :4.500e-07 Median :0.000e+00
## Mean :1.079e-04 Mean :3.337e-05
## 3rd Qu.:7.747e-05 3rd Qu.:4.450e-06
## Max. :3.173e-03 Max. :1.454e-03
## Mediterraneibacter_butyricigenes Mediterraneibacter_sp_NSJ_151
## Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :2.600e-06 Median :0.000e+00
## Mean :3.768e-05 Mean :1.456e-05
## 3rd Qu.:3.192e-05 3rd Qu.:0.000e+00
## Max. :4.621e-04 Max. :3.043e-04
## Methanobrevibacter_smithii Romboutsia_timonensis Ruminococcus_gnavus
## Min. :0.000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.000000 Median :6.500e-07 Median :1.500e-07
## Mean :0.001604 Mean :4.635e-04 Mean :1.062e-03
## 3rd Qu.:0.000000 3rd Qu.:2.556e-04 3rd Qu.:1.167e-04
## Max. :0.099630 Max. :2.028e-02 Max. :1.093e-01
## Ruminococcus_lactaris Ruminococcus_sp_AF41_9 Senegalimassilia_anaerobia
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :3.785e-05 Median :0.0000000 Median :0.000e+00
## Mean :6.396e-04 Mean :0.0002778 Mean :8.710e-05
## 3rd Qu.:6.091e-04 3rd Qu.:0.0000736 3rd Qu.:5.245e-05
## Max. :9.091e-03 Max. :0.0091418 Max. :1.817e-03
## Slackia_isoflavoniconvertens Streptococcus_parasanguinis Veillonella_dispar
## Min. :0.0000000 Min. :0.000e+00 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.000e+00
## Median :0.0000000 Median :2.700e-06 Median :0.000e+00
## Mean :0.0003184 Mean :9.943e-05 Mean :1.182e-04
## 3rd Qu.:0.0002430 3rd Qu.:7.952e-05 3rd Qu.:7.177e-05
## Max. :0.0084554 Max. :1.600e-03 Max. :2.388e-03
## Victivallis_lenta Bifidobacterium_pseudocatenulatum Eubacterium_sp_AF34_35BH
## Min. :0.0000000 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.0000000 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.0000000 Median :0.000e+00 Median :0.0000000
## Mean :0.0003579 Mean :5.605e-04 Mean :0.0001452
## 3rd Qu.:0.0000000 3rd Qu.:3.013e-05 3rd Qu.:0.0000919
## Max. :0.0092131 Max. :1.278e-02 Max. :0.0027871
## Faecalicatena_contorta GGB9559_SGB14969 GGB9759_SGB15370
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.000e+00 Median :0.000e+00 Median :0.0000000
## Mean :1.262e-05 Mean :5.645e-05 Mean :0.0002567
## 3rd Qu.:0.000e+00 3rd Qu.:5.060e-05 3rd Qu.:0.0002142
## Max. :3.469e-04 Max. :6.278e-04 Max. :0.0054074
## Roseburia_lenta Enterocloster_bolteae GGB2848_SGB3813
## Min. :0.0000000 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.0000000 Median :0.0000030 Median :0.000e+00
## Mean :0.0012327 Mean :0.0001893 Mean :3.600e-05
## 3rd Qu.:0.0003235 3rd Qu.:0.0001183 3rd Qu.:2.275e-05
## Max. :0.0412711 Max. :0.0036707 Max. :1.635e-03
## GGB3005_SGB3996 GGB3061_SGB4063 GGB36331_SGB15121
## Min. :0.000e+00 Min. :0.000e+00 Min. :0.0000000
## 1st Qu.:0.000e+00 1st Qu.:0.000e+00 1st Qu.:0.0000000
## Median :0.000e+00 Median :0.000e+00 Median :0.0000000
## Mean :4.229e-05 Mean :4.684e-05 Mean :0.0001415
## 3rd Qu.:2.050e-06 3rd Qu.:2.175e-06 3rd Qu.:0.0000797
## Max. :2.103e-03 Max. :1.154e-03 Max. :0.0021450
## Hungatella_hathewayi TM7_phylum_sp_oral_taxon_352 Veillonella_parvula
## Min. :0.000e+00 Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.000e+00 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.000e+00 Median :0.0000000 Median :0.000e+00
## Mean :1.890e-04 Mean :0.0000476 Mean :2.101e-04
## 3rd Qu.:9.750e-06 3rd Qu.:0.0000476 3rd Qu.:6.352e-05
## Max. :2.653e-02 Max. :0.0011388 Max. :9.409e-03
## GGB6649_SGB9391 Veillonella_atypica
## Min. :0.0000000 Min. :0.000e+00
## 1st Qu.:0.0000000 1st Qu.:0.000e+00
## Median :0.0000000 Median :0.000e+00
## Mean :0.0002582 Mean :9.890e-05
## 3rd Qu.:0.0003208 3rd Qu.:2.483e-05
## Max. :0.0031719 Max. :2.649e-03
data_microbiome_original_raw[1:15, 1:5]
## Sample Country Diet Adlercreutzia_equolifaciens
## 1 T36 CZ VEGAN 0.0000155
## 2 T47 CZ VEGAN 0.0000220
## 3 T55 CZ VEGAN 0.0000103
## 4 T59 CZ VEGAN 0.0000000
## 5 T60 CZ VEGAN 0.0000103
## 6 T61 CZ VEGAN 0.0000000
## 7 T66 CZ VEGAN 0.0000812
## 8 T67 CZ VEGAN 0.0009972
## 9 T68 CZ VEGAN 0.0000146
## 10 T69 CZ VEGAN 0.0002147
## 11 T70 CZ VEGAN 0.0000486
## 12 T71 CZ VEGAN 0.0000000
## 13 T72 CZ VEGAN 0.0000752
## 14 T85 CZ VEGAN 0.0006369
## 15 T86 CZ VEGAN 0.0000000
## Agathobaculum_butyriciproducens
## 1 0.0001334
## 2 0.0066116
## 3 0.0027177
## 4 0.0013599
## 5 0.0010438
## 6 0.0108596
## 7 0.0018825
## 8 0.0078466
## 9 0.0058316
## 10 0.0101227
## 11 0.0005179
## 12 0.0063437
## 13 0.0039945
## 14 0.0069611
## 15 0.00149843.1.2 Validation set
3.1.2.1 Get metadata from lipidom table
Open code
data_lipids_validation <- read.xlsx('gitignore/data/lipidome_validation_cohort.xlsx') %>%
select(X1, X2) %>%
mutate(ID = X1)3.1.2.2 Connect validation data
Open code
data_microbiome_validation_raw <- read.table(
'gitignore/data/0_Data_Metaphlan4_species_filtered_KOMPAS_rel_ab.txt') %>% t()
colnames(data_microbiome_validation_raw) <- data_microbiome_validation_raw[1,]
data_microbiome_validation_raw <- data_microbiome_validation_raw[-1, ] %>% data.frame() %>%
mutate(
ID = paste0("K", gsub("\\..*", "", trimws(ID))),
across(Adlercreutzia_equolifaciens:Veillonella_atypica, ~ as.numeric(.)/100)
) %>%
left_join(data_lipids_validation, by = 'ID') %>%
mutate(Data = 'valid', Sample = ID, Diet = X2) %>%
select(Sample, Data, Diet, everything()) %>%
select(-ID, -X1, -X2)3.1.3 Get center-log transformed value
Open code
## Training data
metadata <- data_microbiome_original_raw[, c("Sample", "Country", "Diet")]
bacteria_data <- data_microbiome_original_raw[, -(1:3)]
clr_bacteria_data <- clr(bacteria_data)
data_microbiome_original <- cbind(metadata, clr_bacteria_data)
## Validation data
metadata <- data_microbiome_validation_raw[, c("Sample", "Data", "Diet")]
bacteria_data <- data_microbiome_validation_raw[, -(1:3)]
clr_bacteria_data <- clr(bacteria_data)
data_microbiome_validation <- cbind(metadata, clr_bacteria_data)3.1.4 Merge training and validation dataset
Open code
common_microbiome <- intersect(
colnames(data_microbiome_original),
colnames(data_microbiome_validation))[-c(1:2)]
tr1 <- data_microbiome_original %>%
mutate(Data = if_else(Country == 'CZ', 'CZ_tr', 'IT_tr')) %>%
select(Data, Diet, all_of(common_microbiome))
tr2 <- data_microbiome_validation %>%
mutate(Data = 'valid',
Diet = Diet) %>%
select(Data, Diet, all_of(common_microbiome))
data_merged <- bind_rows(tr1, tr2)3.2 Explore
3.2.1 Data summary
Open code
summary(data_microbiome_original)
## Sample Country Diet
## Length:166 Length:166 Length:166
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
## Adlercreutzia_equolifaciens Agathobaculum_butyriciproducens
## Min. :-5.3879 Min. :-1.6741
## 1st Qu.:-1.8236 1st Qu.: 0.9966
## Median :-0.3954 Median : 1.7080
## Mean :-0.9361 Mean : 1.6332
## 3rd Qu.: 0.0000 3rd Qu.: 2.3623
## Max. : 2.9097 Max. : 4.1360
## Akkermansia_muciniphila Alistipes_communis Alistipes_finegoldii
## Min. :-5.961 Min. :-4.579 Min. :-5.9534
## 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.0000
## Median : 1.018 Median : 1.911 Median : 0.4529
## Mean : 1.437 Mean : 1.666 Mean : 0.8876
## 3rd Qu.: 3.155 3rd Qu.: 2.925 3rd Qu.: 2.0030
## Max. : 7.112 Max. : 5.808 Max. : 5.2364
## Alistipes_ihumii Alistipes_indistinctus Alistipes_onderdonkii
## Min. :-4.4586 Min. :-5.34668 Min. :-5.68594
## 1st Qu.: 0.0000 1st Qu.:-0.46130 1st Qu.: 0.02463
## Median : 0.1777 Median : 0.00000 Median : 2.08366
## Mean : 0.8382 Mean :-0.05192 Mean : 1.83492
## 3rd Qu.: 1.8759 3rd Qu.: 0.60784 3rd Qu.: 3.50525
## Max. : 4.4281 Max. : 3.54569 Max. : 6.75375
## Alistipes_putredinis Alistipes_senegalensis Alistipes_shahii
## Min. :-7.606 Min. :-5.4138 Min. :-6.235
## 1st Qu.: 1.605 1st Qu.: 0.0000 1st Qu.: 0.917
## Median : 3.783 Median : 0.0000 Median : 2.579
## Mean : 2.960 Mean : 0.2239 Mean : 2.249
## 3rd Qu.: 4.945 3rd Qu.: 0.7422 3rd Qu.: 3.601
## Max. : 6.531 Max. : 4.9916 Max. : 5.574
## Anaerobutyricum_hallii Anaerofilum_hominis Anaeromassilibacillus_senegalensis
## Min. :-6.53505 Min. :-6.448 Min. :-6.027
## 1st Qu.:-0.53293 1st Qu.:-2.698 1st Qu.:-2.005
## Median : 0.00000 Median : 0.000 Median :-0.154
## Mean :-0.04001 Mean :-1.190 Mean :-1.108
## 3rd Qu.: 1.03361 3rd Qu.: 0.000 3rd Qu.: 0.000
## Max. : 2.70957 Max. : 1.493 Max. : 2.877
## Anaerostipes_hadrus Anaerotignum_faecicola Anaerotruncus_colihominis
## Min. :-6.0832 Min. :-5.55638 Min. :-5.1760
## 1st Qu.:-0.2503 1st Qu.:-0.02553 1st Qu.:-1.2463
## Median : 0.7114 Median : 0.00000 Median : 0.0000
## Mean : 0.5021 Mean : 0.31693 Mean :-0.7356
## 3rd Qu.: 1.9325 3rd Qu.: 1.12255 3rd Qu.: 0.0000
## Max. : 4.6126 Max. : 3.53207 Max. : 1.8766
## Anaerotruncus_massiliensis Anaerotruncus_rubiinfantis Bacteroides_caccae
## Min. :-5.8087 Min. :-6.8486 Min. :-7.0322
## 1st Qu.: 0.0000 1st Qu.:-1.8683 1st Qu.: 0.0000
## Median : 0.0000 Median :-0.3007 Median : 0.7947
## Mean :-0.5276 Mean :-1.0680 Mean : 1.1023
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 2.3678
## Max. : 1.8737 Max. : 0.4163 Max. : 5.5946
## Bacteroides_cellulosilyticus Bacteroides_clarus Bacteroides_eggerthii
## Min. :-6.5276 Min. :-5.87834 Min. :-5.8104
## 1st Qu.: 0.0000 1st Qu.: 0.00000 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.00000 Median : 0.0000
## Mean : 0.3400 Mean : 0.02645 Mean : 0.1948
## 3rd Qu.: 0.7151 3rd Qu.: 0.00000 3rd Qu.: 0.7557
## Max. : 5.5202 Max. : 5.54521 Max. : 5.1987
## Bacteroides_fragilis Bacteroides_ovatus Bacteroides_stercoris
## Min. :-4.1363 Min. :-4.48695 Min. :-5.6643
## 1st Qu.: 0.0000 1st Qu.: 0.08505 1st Qu.: 0.0000
## Median : 0.0000 Median : 1.49041 Median : 0.0000
## Mean : 0.1575 Mean : 1.38139 Mean : 0.7809
## 3rd Qu.: 0.0000 3rd Qu.: 2.77379 3rd Qu.: 2.3743
## Max. : 4.2877 Max. : 5.60476 Max. : 5.8632
## Bacteroides_thetaiotaomicron Bacteroides_uniformis Bacteroides_xylanisolvens
## Min. :-5.9862 Min. :-4.205 Min. :-4.4018
## 1st Qu.:-0.4044 1st Qu.: 2.439 1st Qu.:-0.4428
## Median : 0.3483 Median : 3.601 Median : 0.0000
## Mean : 0.3787 Mean : 3.421 Mean : 0.2817
## 3rd Qu.: 1.7410 3rd Qu.: 4.620 3rd Qu.: 1.2479
## Max. : 4.6917 Max. : 6.136 Max. : 4.9017
## Barnesiella_intestinihominis Bifidobacterium_adolescentis
## Min. :-4.622 Min. :-5.687
## 1st Qu.: 0.000 1st Qu.: 0.000
## Median : 1.149 Median : 1.780
## Mean : 1.137 Mean : 1.413
## 3rd Qu.: 2.178 3rd Qu.: 3.042
## Max. : 4.642 Max. : 5.701
## Bifidobacterium_longum Bilophila_SGB15451 Bilophila_wadsworthia
## Min. :-4.802 Min. :-5.0800 Min. :-5.3209
## 1st Qu.: 0.000 1st Qu.: 0.0000 1st Qu.:-0.2692
## Median : 1.278 Median : 0.0000 Median : 0.4433
## Mean : 1.261 Mean :-0.2986 Mean : 0.4978
## 3rd Qu.: 2.186 3rd Qu.: 0.0000 3rd Qu.: 1.5429
## Max. : 6.492 Max. : 2.8823 Max. : 4.0864
## Blautia_faecis Blautia_glucerasea Blautia_massiliensis Blautia_obeum
## Min. :-4.88005 Min. :-6.4562 Min. :-7.3557 Min. :-5.2312
## 1st Qu.:-0.83153 1st Qu.:-1.1658 1st Qu.:-0.6892 1st Qu.:-1.0399
## Median : 0.00000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.08774 Mean :-0.5844 Mean :-0.1389 Mean :-0.2131
## 3rd Qu.: 0.87471 3rd Qu.: 0.2766 3rd Qu.: 0.8917 3rd Qu.: 0.6754
## Max. : 4.39225 Max. : 2.6244 Max. : 4.3965 Max. : 3.6839
## Blautia_sp_MCC283 Blautia_wexlerae Brotolimicola_acetigignens
## Min. :-5.6218 Min. :-5.8602 Min. :-3.716
## 1st Qu.:-1.0715 1st Qu.:-0.4109 1st Qu.: 0.000
## Median : 0.0000 Median : 1.1615 Median : 1.153
## Mean :-0.2482 Mean : 0.7826 Mean : 1.206
## 3rd Qu.: 0.4179 3rd Qu.: 2.1478 3rd Qu.: 2.560
## Max. : 3.7660 Max. : 4.9687 Max. : 5.090
## Butyricimonas_faecihominis Butyricimonas_virosa
## Min. :-5.1290 Min. :-5.8793
## 1st Qu.:-0.4997 1st Qu.:-0.7518
## Median : 0.0000 Median : 0.0000
## Mean :-0.3321 Mean :-0.5573
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 2.2716 Max. : 1.6800
## Candidatus_Borkfalkia_ceftriaxoniphila Candidatus_Cibionibacter_quicibialis
## Min. :-5.7494 Min. :-2.997
## 1st Qu.: 0.0000 1st Qu.: 1.750
## Median : 0.0000 Median : 2.884
## Mean :-0.1109 Mean : 2.828
## 3rd Qu.: 0.0000 3rd Qu.: 4.004
## Max. : 2.8325 Max. : 6.222
## Clostridia_bacterium_UC5_1_1D1 Clostridiaceae_bacterium
## Min. :-5.4364 Min. :-4.788408
## 1st Qu.:-2.3233 1st Qu.:-0.000219
## Median :-0.4205 Median : 1.075284
## Mean :-1.1843 Mean : 0.759460
## 3rd Qu.: 0.0000 3rd Qu.: 1.911031
## Max. : 0.5711 Max. : 3.368168
## Clostridiaceae_bacterium_AF18_31LB Clostridiaceae_bacterium_Marseille_Q4143
## Min. :-5.8178 Min. :-6.4472
## 1st Qu.:-1.1227 1st Qu.:-1.9792
## Median :-0.1195 Median :-0.6454
## Mean :-0.4046 Mean :-1.0371
## 3rd Qu.: 0.2689 3rd Qu.: 0.0000
## Max. : 2.9192 Max. : 1.4063
## Clostridiaceae_bacterium_Marseille_Q4145 Clostridiales_bacterium
## Min. :-6.1207 Min. :-4.63910
## 1st Qu.:-1.8869 1st Qu.:-0.92139
## Median :-0.7634 Median : 0.00000
## Mean :-1.1618 Mean : 0.02174
## 3rd Qu.: 0.0000 3rd Qu.: 1.00087
## Max. : 0.6652 Max. : 4.09011
## Clostridiales_bacterium_KLE1615 Clostridium_SGB4750 Clostridium_SGB4909
## Min. :-4.9682 Min. :-5.0596 Min. :-5.7795
## 1st Qu.:-0.4299 1st Qu.:-1.5247 1st Qu.:-0.6520
## Median : 0.2944 Median : 0.0000 Median : 0.0000
## Mean : 0.1387 Mean :-0.5647 Mean :-0.4153
## 3rd Qu.: 1.1507 3rd Qu.: 0.1326 3rd Qu.: 0.0000
## Max. : 3.0587 Max. : 3.3859 Max. : 4.0898
## Clostridium_fessum Clostridium_leptum Clostridium_sp_AF20_17LB
## Min. :-5.976 Min. :-5.2099 Min. :-5.45520
## 1st Qu.: 0.565 1st Qu.:-2.0180 1st Qu.:-0.50576
## Median : 1.418 Median :-0.4343 Median : 0.00000
## Mean : 1.307 Mean :-0.9416 Mean : 0.03637
## 3rd Qu.: 2.094 3rd Qu.: 0.0000 3rd Qu.: 1.19653
## Max. : 4.349 Max. : 3.3064 Max. : 3.09209
## Clostridium_sp_AF27_2AA Clostridium_sp_AF36_4 Clostridium_sp_AM22_11AC
## Min. :-4.5182 Min. :-6.1933 Min. :-3.6428
## 1st Qu.:-0.8515 1st Qu.:-0.2940 1st Qu.:-0.3825
## Median : 0.0000 Median : 0.0000 Median : 0.4232
## Mean :-0.2568 Mean : 0.3057 Mean : 0.4568
## 3rd Qu.: 0.2150 3rd Qu.: 1.4536 3rd Qu.: 1.4361
## Max. : 2.7417 Max. : 4.7043 Max. : 3.3216
## Clostridium_sp_AM33_3 Collinsella_aerofaciens Coprobacter_fastidiosus
## Min. :-4.06890 Min. :-1.8321 Min. :-6.0734
## 1st Qu.:-0.40458 1st Qu.: 0.0000 1st Qu.:-0.6383
## Median : 0.00000 Median : 0.8381 Median : 0.0000
## Mean :-0.01868 Mean : 0.8620 Mean :-0.5113
## 3rd Qu.: 0.56758 3rd Qu.: 1.6157 3rd Qu.: 0.0000
## Max. : 2.86121 Max. : 3.9768 Max. : 2.5060
## Coprococcus_catus Coprococcus_comes Coprococcus_eutactus Dorea_formicigenerans
## Min. :-5.1965 Min. :-5.2215 Min. :-6.1262 Min. :-5.6458
## 1st Qu.:-0.8594 1st Qu.:-0.6394 1st Qu.: 0.0000 1st Qu.:-1.1649
## Median : 0.0000 Median : 0.0000 Median : 0.9813 Median : 0.0000
## Mean :-0.3717 Mean :-0.1285 Mean : 1.2233 Mean :-0.5043
## 3rd Qu.: 0.3124 3rd Qu.: 0.6050 3rd Qu.: 2.4333 3rd Qu.: 0.2688
## Max. : 2.4296 Max. : 3.2415 Max. : 6.0710 Max. : 2.0020
## Dorea_longicatena Dorea_sp_AF36_15AT Dysosmobacter_SGB15077
## Min. :-4.9302 Min. :-6.7063 Min. :-6.4363
## 1st Qu.:-0.6733 1st Qu.:-2.0437 1st Qu.: 0.0000
## Median : 0.2830 Median :-0.7004 Median : 0.0000
## Mean : 0.1425 Mean :-1.1400 Mean :-0.4436
## 3rd Qu.: 1.3986 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 3.3803 Max. : 0.9716 Max. : 3.8869
## Dysosmobacter_welbionis Eggerthella_lenta Enterocloster_citroniae
## Min. :-4.0071 Min. :-6.4774 Min. :-6.0016
## 1st Qu.: 0.0000 1st Qu.:-1.2018 1st Qu.:-1.8957
## Median : 0.9038 Median : 0.0000 Median :-0.8421
## Mean : 0.9727 Mean :-0.8392 Mean :-1.1850
## 3rd Qu.: 2.3094 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 5.0330 Max. : 1.4281 Max. : 0.7546
## Enterocloster_hominis Escherichia_coli Eubacterium_ramulus
## Min. :-4.60696 Min. :-4.9322 Min. :-6.2096
## 1st Qu.: 0.00000 1st Qu.:-1.1396 1st Qu.:-1.4087
## Median : 0.00000 Median : 0.0000 Median :-0.3327
## Mean :-0.09605 Mean :-0.1907 Mean :-0.7996
## 3rd Qu.: 0.00000 3rd Qu.: 0.5415 3rd Qu.: 0.0000
## Max. : 3.59139 Max. : 4.6124 Max. : 1.7837
## Eubacterium_rectale Eubacterium_siraeum Eubacterium_ventriosum
## Min. :-6.790 Min. :-6.4360 Min. :-5.5382
## 1st Qu.: 1.227 1st Qu.:-0.2593 1st Qu.:-1.0211
## Median : 2.596 Median : 0.0000 Median : 0.0000
## Mean : 2.240 Mean :-0.1503 Mean :-0.3966
## 3rd Qu.: 3.648 3rd Qu.: 0.0000 3rd Qu.: 0.3953
## Max. : 5.434 Max. : 4.4675 Max. : 2.7794
## Faecalibacterium_SGB15346 Faecalibacterium_prausnitzii
## Min. :-6.1955 Min. :-4.639
## 1st Qu.: 0.3215 1st Qu.: 3.844
## Median : 1.8232 Median : 4.481
## Mean : 1.5416 Mean : 4.471
## 3rd Qu.: 3.2713 3rd Qu.: 5.338
## Max. : 5.7360 Max. : 6.786
## Faecalibacterium_sp_CLA_AA_H233 Faecalibacterium_sp_HTFF
## Min. :-5.8488 Min. :-6.3530
## 1st Qu.:-0.9810 1st Qu.:-0.2376
## Median : 0.0000 Median : 0.0000
## Mean : 0.0375 Mean : 0.0274
## 3rd Qu.: 1.3638 3rd Qu.: 0.9419
## Max. : 5.2997 Max. : 4.2136
## Faecalicatena_fissicatena Flavonifractor_plautii
## Min. :-5.3392 Min. :-5.1080
## 1st Qu.:-0.2981 1st Qu.:-1.1648
## Median : 0.0000 Median : 0.0000
## Mean : 0.1068 Mean :-0.1363
## 3rd Qu.: 0.9194 3rd Qu.: 1.0215
## Max. : 3.1942 Max. : 3.2732
## Fusicatenibacter_saccharivorans Fusicatenibacter_sp_CLA_AA_H277
## Min. :-7.102 Min. :-4.6991
## 1st Qu.: 1.090 1st Qu.:-1.2460
## Median : 1.820 Median :-0.1455
## Mean : 1.677 Mean :-0.4842
## 3rd Qu.: 2.438 3rd Qu.: 0.2713
## Max. : 4.882 Max. : 2.3209
## GGB13404_SGB14252 GGB1420_SGB1957 GGB2653_SGB3574 GGB2998_SGB3988
## Min. :-5.9397 Min. :-4.53110 Min. :-6.5200 Min. :-5.1524
## 1st Qu.:-0.7179 1st Qu.: 0.00000 1st Qu.:-1.7597 1st Qu.:-1.1401
## Median : 0.0000 Median : 0.00000 Median :-0.4100 Median : 0.0000
## Mean :-0.5002 Mean : 0.03005 Mean :-0.9612 Mean :-0.5979
## 3rd Qu.: 0.0000 3rd Qu.: 0.00000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 2.0974 Max. : 2.98099 Max. : 2.0777 Max. : 1.9321
## GGB3034_SGB4030 GGB3109_SGB4121 GGB3175_SGB4191 GGB33469_SGB15236
## Min. :-5.6446 Min. :-4.6465 Min. :-4.7615 Min. :-6.2739
## 1st Qu.: 0.0000 1st Qu.:-0.7139 1st Qu.: 0.0000 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.5141 Mean :-0.3088 Mean : 0.4437 Mean : 0.2968
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.1534 3rd Qu.: 1.1847
## Max. : 0.0000 Max. : 2.4504 Max. : 5.1548 Max. : 5.4452
## GGB33512_SGB15203 GGB33586_SGB53517 GGB3537_SGB4727 GGB38744_SGB14842
## Min. :-3.856 Min. :-4.2678 Min. :-5.4365 Min. :-5.8953
## 1st Qu.: 0.000 1st Qu.:-0.4349 1st Qu.:-1.1792 1st Qu.: 0.0000
## Median : 0.000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.124 Mean :-0.3506 Mean :-0.6529 Mean :-0.6669
## 3rd Qu.: 0.000 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 4.904 Max. : 2.7969 Max. : 0.9486 Max. : 0.0000
## GGB45432_SGB63101 GGB45613_SGB63326 GGB47687_SGB2286 GGB52106_SGB72838
## Min. :-5.6970 Min. :-6.593 Min. :-5.8572 Min. :-4.7965
## 1st Qu.:-2.4242 1st Qu.:-2.669 1st Qu.: 0.0000 1st Qu.:-0.5314
## Median :-0.5422 Median : 0.000 Median : 0.0000 Median : 0.0000
## Mean :-1.2638 Mean :-1.193 Mean : 0.5912 Mean :-0.5016
## 3rd Qu.: 0.0000 3rd Qu.: 0.000 3rd Qu.: 0.8481 3rd Qu.: 0.0000
## Max. : 0.3327 Max. : 0.000 Max. : 6.1121 Max. : 1.3288
## GGB52130_SGB14966 GGB9062_SGB13981 GGB9063_SGB13982 GGB9064_SGB13983
## Min. :-4.5439 Min. :-5.4098 Min. :-3.34675 Min. :-4.67933
## 1st Qu.:-1.2764 1st Qu.: 0.0000 1st Qu.: 0.00000 1st Qu.: 0.00000
## Median : 0.0000 Median : 0.0000 Median : 0.00000 Median : 0.00000
## Mean :-0.6277 Mean :-0.2607 Mean : 0.04859 Mean :-0.04388
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.00000 3rd Qu.: 0.00000
## Max. : 1.6962 Max. : 2.2215 Max. : 4.07597 Max. : 3.90533
## GGB9342_SGB14306 GGB9345_SGB14311 GGB9453_SGB14844 GGB9502_SGB14899
## Min. :-5.6136 Min. :-6.6626 Min. :-5.3761 Min. :-4.40294
## 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.00000
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.00000
## Mean : 0.3031 Mean : 0.4204 Mean :-0.4094 Mean : 0.01852
## 3rd Qu.: 1.0113 3rd Qu.: 0.8474 3rd Qu.: 0.0000 3rd Qu.: 0.01587
## Max. : 4.7917 Max. : 4.8035 Max. : 4.1317 Max. : 2.52621
## GGB9509_SGB14906 GGB9522_SGB14921 GGB9531_SGB14932 GGB9534_SGB14937
## Min. :-5.20406 Min. :-4.7720 Min. :-4.8496 Min. :-6.1275
## 1st Qu.: 0.00000 1st Qu.:-1.2779 1st Qu.:-0.1129 1st Qu.:-1.2666
## Median : 0.00000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.05643 Mean :-0.6737 Mean :-0.3279 Mean :-0.5408
## 3rd Qu.: 0.00000 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 4.75064 Max. : 2.2978 Max. : 1.8710 Max. : 3.6275
## GGB9602_SGB15031 GGB9614_SGB15049 GGB9619_SGB15067 GGB9621_SGB15073
## Min. :-5.0226 Min. :-5.6756 Min. :-4.9466 Min. :-3.731002
## 1st Qu.: 0.0000 1st Qu.:-0.2012 1st Qu.:-0.3116 1st Qu.: 0.000000
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.000000
## Mean : 0.5927 Mean : 0.2718 Mean :-0.3647 Mean :-0.006089
## 3rd Qu.: 1.3147 3rd Qu.: 1.2096 3rd Qu.: 0.0000 3rd Qu.: 0.028730
## Max. : 5.6397 Max. : 3.3567 Max. : 2.3513 Max. : 2.402629
## GGB9635_SGB15106 GGB9646_SGB15123 GGB9667_SGB15164 GGB9699_SGB15216
## Min. :-4.256 Min. :-5.3458 Min. :-5.5620 Min. :-5.9559
## 1st Qu.: 0.000 1st Qu.:-1.5106 1st Qu.:-0.3300 1st Qu.:-0.5640
## Median : 0.000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 1.358 Mean :-0.8929 Mean :-0.1921 Mean : 0.3048
## 3rd Qu.: 3.116 3rd Qu.: 0.0000 3rd Qu.: 0.0153 3rd Qu.: 1.5112
## Max. : 6.405 Max. : 2.0239 Max. : 3.0430 Max. : 4.1608
## GGB9708_SGB15234 GGB9715_SGB15265 GGB9719_SGB15272 GGB9719_SGB15273
## Min. :-6.1955 Min. :-4.808 Min. :-4.2084 Min. :-4.0738
## 1st Qu.: 0.0000 1st Qu.: 0.000 1st Qu.:-0.9183 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.000 Median : 0.0000 Median : 0.0000
## Mean : 0.6971 Mean : 1.080 Mean :-0.4853 Mean :-0.3027
## 3rd Qu.: 1.9222 3rd Qu.: 2.875 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 5.5223 Max. : 5.683 Max. : 2.4982 Max. : 1.6065
## GGB9730_SGB15291 GGB9758_SGB15368 GGB9760_SGB15373 GGB9765_SGB15382
## Min. :-3.29380 Min. :-6.406 Min. :-3.4466 Min. :-5.2182
## 1st Qu.:-0.08604 1st Qu.: 0.000 1st Qu.:-0.2374 1st Qu.:-0.1042
## Median : 0.10778 Median : 1.351 Median : 0.0000 Median : 0.0000
## Mean : 0.48088 Mean : 1.804 Mean : 0.2687 Mean :-0.5102
## 3rd Qu.: 1.41027 3rd Qu.: 4.179 3rd Qu.: 0.8841 3rd Qu.: 0.0000
## Max. : 3.79637 Max. : 7.262 Max. : 3.6974 Max. : 2.0323
## GGB9770_SGB15390 GGB9775_SGB15395 GGB9781_SGB15402 GGB9818_SGB15459
## Min. :-5.7452 Min. :-4.87045 Min. :-5.6270 Min. :-6.3782
## 1st Qu.: 0.0000 1st Qu.: 0.00000 1st Qu.:-0.2432 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.00000 Median : 0.0000 Median : 0.0000
## Mean :-0.3464 Mean : 0.07391 Mean :-0.6731 Mean :-0.1181
## 3rd Qu.: 0.0000 3rd Qu.: 0.00000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 2.7494 Max. : 3.16872 Max. : 0.5314 Max. : 3.1263
## Gemmiger_formicilis Guopingia_tenuis Holdemania_filiformis
## Min. :-5.551 Min. :-5.8281 Min. :-5.709
## 1st Qu.: 1.689 1st Qu.:-2.2014 1st Qu.:-1.619
## Median : 2.593 Median : 0.0000 Median : 0.000
## Mean : 2.344 Mean :-1.1973 Mean :-0.830
## 3rd Qu.: 3.434 3rd Qu.: 0.0000 3rd Qu.: 0.000
## Max. : 5.954 Max. : 0.2643 Max. : 1.297
## Hydrogenoanaerobacterium_saccharovorans Intestinimonas_butyriciproducens
## Min. :-5.8536 Min. :-4.8159
## 1st Qu.: 0.0000 1st Qu.:-1.5908
## Median : 0.1442 Median :-0.1448
## Mean : 0.4071 Mean :-0.7856
## 3rd Qu.: 1.0568 3rd Qu.: 0.0000
## Max. : 3.2497 Max. : 3.4351
## Intestinimonas_gabonensis Intestinimonas_massiliensis
## Min. :-5.5297 Min. :-5.3991
## 1st Qu.:-1.8054 1st Qu.:-0.9673
## Median :-0.6880 Median : 0.0000
## Mean :-1.0503 Mean :-0.4469
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 0.8567 Max. : 3.2466
## Lachnoclostridium_sp_An138 Lachnospira_eligens Lachnospira_pectinoschiza
## Min. :-6.1261 Min. :-4.0601 Min. :-6.0273
## 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.3644
## Median : 0.0000 Median : 0.9611 Median : 1.8097
## Mean :-0.6742 Mean : 1.1226 Mean : 1.6724
## 3rd Qu.: 0.0000 3rd Qu.: 2.5593 3rd Qu.: 2.9930
## Max. : 0.0000 Max. : 5.1842 Max. : 5.8982
## Lachnospiraceae_bacterium Lachnospiraceae_bacterium_AM48_27BH
## Min. :-4.78137 Min. :-6.2761
## 1st Qu.:-0.95541 1st Qu.:-0.9196
## Median : 0.00000 Median : 0.0000
## Mean : 0.04254 Mean :-0.3611
## 3rd Qu.: 1.26166 3rd Qu.: 0.4298
## Max. : 3.82406 Max. : 2.4490
## Lachnospiraceae_bacterium_CLA_AA_H215 Lachnospiraceae_bacterium_CLA_AA_H244
## Min. :-6.3304 Min. :-3.862
## 1st Qu.:-1.3246 1st Qu.: 0.000
## Median : 0.0000 Median : 1.061
## Mean :-0.7616 Mean : 1.040
## 3rd Qu.: 0.0000 3rd Qu.: 1.867
## Max. : 1.8505 Max. : 4.322
## Lachnotalea_sp_AF33_28 Lacrimispora_amygdalina Lawsonibacter_SGB15145
## Min. :-6.7757 Min. :-5.8052 Min. :-5.4121
## 1st Qu.:-2.6374 1st Qu.:-0.2405 1st Qu.:-0.5174
## Median : 0.0000 Median : 0.5614 Median : 0.0000
## Mean :-1.3435 Mean : 0.4253 Mean :-0.3279
## 3rd Qu.: 0.0000 3rd Qu.: 1.4613 3rd Qu.: 0.1997
## Max. : 0.0807 Max. : 2.8836 Max. : 2.6373
## Lawsonibacter_asaccharolyticus Lawsonibacter_hominis Ligaoa_zhengdingensis
## Min. :-4.7540 Min. :-6.1852 Min. :-6.6062
## 1st Qu.:-0.5325 1st Qu.:-1.2074 1st Qu.:-1.4531
## Median : 0.2685 Median : 0.0000 Median : 0.0000
## Mean : 0.4549 Mean :-0.5602 Mean :-0.9759
## 3rd Qu.: 1.8395 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 4.6691 Max. : 3.0564 Max. : 0.0000
## Mediterraneibacter_faecis Odoribacter_splanchnicus Oliverpabstia_intestinalis
## Min. :-5.2996 Min. :-3.9411 Min. :-5.2171
## 1st Qu.:-1.0579 1st Qu.: 0.0000 1st Qu.:-0.7777
## Median : 0.0000 Median : 0.8127 Median : 0.0000
## Mean :-0.4471 Mean : 0.7651 Mean :-0.2479
## 3rd Qu.: 0.2132 3rd Qu.: 1.6757 3rd Qu.: 0.0000
## Max. : 2.7140 Max. : 3.0476 Max. : 3.5413
## Oscillibacter_sp_ER4 Oscillibacter_sp_MSJ_31 Oscillibacter_sp_PC13
## Min. :-4.295 Min. :-5.907 Min. :-5.987
## 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.:-2.312
## Median : 2.384 Median : 1.049 Median : 0.000
## Mean : 2.086 Mean : 1.219 Mean :-1.180
## 3rd Qu.: 3.484 3rd Qu.: 3.039 3rd Qu.: 0.000
## Max. : 5.434 Max. : 6.375 Max. : 0.000
## Oscillibacter_valericigenes Oscillospiraceae_bacterium
## Min. :-4.473 Min. :-4.7967
## 1st Qu.: 0.320 1st Qu.:-0.1854
## Median : 1.493 Median : 0.0000
## Mean : 1.362 Mean : 0.3729
## 3rd Qu.: 2.509 3rd Qu.: 1.1587
## Max. : 5.262 Max. : 5.2059
## Oscillospiraceae_bacterium_CLA_AA_H250
## Min. :-4.54411
## 1st Qu.:-0.06459
## Median : 0.05668
## Mean : 0.45041
## 3rd Qu.: 1.30189
## Max. : 3.89644
## Oscillospiraceae_bacterium_Marseille_Q3528 Parabacteroides_distasonis
## Min. :-6.02552 Min. :-2.5911
## 1st Qu.:-1.05026 1st Qu.: 0.6096
## Median :-0.08802 Median : 1.6607
## Mean :-0.49883 Mean : 1.5234
## 3rd Qu.: 0.00000 3rd Qu.: 2.5314
## Max. : 2.23785 Max. : 4.2565
## Parabacteroides_merdae Paraprevotella_clara Parasutterella_excrementihominis
## Min. :-2.585 Min. :-7.582 Min. :-5.70562
## 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.:-0.58426
## Median : 1.692 Median : 0.000 Median : 0.00000
## Mean : 1.472 Mean : 0.684 Mean :-0.04083
## 3rd Qu.: 2.578 3rd Qu.: 2.521 3rd Qu.: 0.79667
## Max. : 4.516 Max. : 4.977 Max. : 3.91225
## Phascolarctobacterium_faecium Phocaeicola_dorei Phocaeicola_sartorii
## Min. :-4.1832 Min. :-5.6214 Min. :-5.5937
## 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.:-1.7440
## Median : 0.0000 Median : 0.7572 Median : 0.0000
## Mean : 0.6681 Mean : 1.1729 Mean :-0.8716
## 3rd Qu.: 1.3949 3rd Qu.: 3.0747 3rd Qu.: 0.0000
## Max. : 5.3883 Max. : 6.1807 Max. : 0.0000
## Phocaeicola_vulgatus Phocea_massiliensis Provencibacterium_massiliense
## Min. :-5.741 Min. :-5.1282 Min. :-6.898
## 1st Qu.: 2.321 1st Qu.:-1.3210 1st Qu.:-1.647
## Median : 3.299 Median : 0.0000 Median : 0.000
## Mean : 3.020 Mean :-0.7528 Mean :-0.873
## 3rd Qu.: 4.483 3rd Qu.: 0.0000 3rd Qu.: 0.000
## Max. : 6.213 Max. : 1.1089 Max. : 0.000
## Pseudoflavonifractor_capillosus Roseburia_faecis Roseburia_hominis
## Min. :-5.4129 Min. :-7.226 Min. :-5.944
## 1st Qu.:-1.4330 1st Qu.: 0.000 1st Qu.: 0.000
## Median : 0.0000 Median : 1.162 Median : 1.223
## Mean :-0.6951 Mean : 1.199 Mean : 1.133
## 3rd Qu.: 0.0000 3rd Qu.: 2.552 3rd Qu.: 2.280
## Max. : 3.7610 Max. : 5.930 Max. : 4.916
## Roseburia_intestinalis Roseburia_inulinivorans Ruminococcus_bicirculans
## Min. :-5.17217 Min. :-5.8540 Min. :-5.0535
## 1st Qu.:-0.22793 1st Qu.:-0.1915 1st Qu.: 0.0000
## Median : 0.00000 Median : 0.9222 Median : 0.4475
## Mean : 0.08328 Mean : 0.7964 Mean : 0.7507
## 3rd Qu.: 1.09541 3rd Qu.: 2.0758 3rd Qu.: 1.9562
## Max. : 4.72592 Max. : 4.7512 Max. : 4.6842
## Ruminococcus_bromii Ruminococcus_torques Ruthenibacterium_lactatiformans
## Min. :-5.769 Min. :-6.2174 Min. :-2.9670
## 1st Qu.: 0.000 1st Qu.:-0.7056 1st Qu.:-0.4346
## Median : 1.089 Median : 0.0000 Median : 0.2900
## Mean : 1.252 Mean :-0.4239 Mean : 0.3920
## 3rd Qu.: 2.710 3rd Qu.: 0.0000 3rd Qu.: 1.1876
## Max. : 5.144 Max. : 2.6706 Max. : 4.8960
## Segatella_copri Simiaoa_sunii Streptococcus_salivarius
## Min. :-6.121 Min. :-4.7315 Min. :-5.6677
## 1st Qu.: 0.000 1st Qu.:-1.0608 1st Qu.:-1.8696
## Median : 0.000 Median : 0.0000 Median :-0.2559
## Mean : 1.093 Mean : 0.2712 Mean :-0.9178
## 3rd Qu.: 2.186 3rd Qu.: 1.6911 3rd Qu.: 0.0000
## Max. : 8.859 Max. : 5.7028 Max. : 2.6156
## Streptococcus_thermophilus Sutterella_wadsworthensis Vescimonas_coprocola
## Min. :-4.2691 Min. :-6.6268 Min. :-3.6998
## 1st Qu.:-0.2553 1st Qu.: 0.0000 1st Qu.:-0.3805
## Median : 0.0000 Median : 0.1828 Median : 0.0000
## Mean :-0.3109 Mean : 1.2046 Mean : 0.3509
## 3rd Qu.: 0.0000 3rd Qu.: 3.1077 3rd Qu.: 1.5151
## Max. : 3.1085 Max. : 5.7922 Max. : 4.3114
## Wansuia_hejianensis Youxingia_wuxianensis bacterium_210917_DFI_7_65
## Min. :-7.195 Min. :-7.385 Min. :-6.1955
## 1st Qu.:-3.003 1st Qu.:-2.699 1st Qu.:-1.0582
## Median : 0.000 Median : 0.000 Median : 0.0000
## Mean :-1.400 Mean :-1.337 Mean :-0.5379
## 3rd Qu.: 0.000 3rd Qu.: 0.000 3rd Qu.: 0.0000
## Max. : 0.000 Max. : 0.000 Max. : 1.7357
## Bacteroides_faecis Clostridiaceae_unclassified_SGB4771 Clostridium_sp_AM49_4BH
## Min. :-6.9192 Min. :-6.6655 Min. :-5.5937
## 1st Qu.: 0.0000 1st Qu.:-0.4258 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.4013 Mean :-0.3298 Mean : 0.1470
## 3rd Qu.: 0.4889 3rd Qu.: 0.0000 3rd Qu.: 0.6252
## Max. : 5.0083 Max. : 3.1516 Max. : 3.6837
## Colidextribacter_sp_210702_DFI_3_9 Enterocloster_lavalensis GGB2982_SGB3964
## Min. :-4.6854 Min. :-6.4898 Min. :-5.4601
## 1st Qu.:-0.7781 1st Qu.:-1.6643 1st Qu.:-0.8472
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.5236 Mean :-0.9849 Mean :-0.4751
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 1.9906 Max. : 0.3161 Max. : 1.8903
## GGB3304_SGB4367 GGB3619_SGB4894 GGB9296_SGB14253 GGB9524_SGB14924
## Min. :-5.9559 Min. :-3.8900 Min. :-4.9269 Min. :-4.2068
## 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.:-0.0594
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.8212 Mean :-0.1701 Mean :-0.1924 Mean :-0.2527
## 3rd Qu.: 2.4033 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 5.5587 Max. : 3.7075 Max. : 2.6320 Max. : 3.9873
## GGB9574_SGB14987 GGB9619_SGB15066 GGB9707_SGB15229 GGB9708_SGB15233
## Min. :-6.0739 Min. :-6.6626 Min. :-3.1017 Min. :-6.45619
## 1st Qu.:-1.1269 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.00000
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.00000
## Mean :-0.7441 Mean :-0.3097 Mean : 0.5169 Mean :-0.03637
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 1.2956 3rd Qu.: 0.02548
## Max. : 0.6636 Max. : 1.8983 Max. : 4.1015 Max. : 5.58215
## GGB9760_SGB15374 Roseburia_sp_AF02_12 Segatella_brunsvicensis
## Min. :-5.7911 Min. :-5.0396 Min. :-6.4159
## 1st Qu.: 0.0000 1st Qu.:-1.0317 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.1243 Mean :-0.3165 Mean : 0.1079
## 3rd Qu.: 0.3593 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 3.5431 Max. : 4.0833 Max. : 8.5476
## Wujia_chipingensis Alistipes_dispar Alistipes_sp_AF17_16
## Min. :-6.7006 Min. :-4.8419 Min. :-4.0321
## 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.4702 Mean : 0.1859 Mean : 0.2998
## 3rd Qu.: 1.5460 3rd Qu.: 0.0000 3rd Qu.: 0.5336
## Max. : 5.0594 Max. : 4.0537 Max. : 4.4258
## Anaerobutyricum_soehngenii Anaerosacchariphilus_sp_NSJ_68
## Min. :-5.3029 Min. :-6.6105
## 1st Qu.:-0.8211 1st Qu.:-2.1414
## Median : 0.0000 Median : 0.0000
## Mean :-0.6380 Mean :-1.1408
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 2.7147 Max. : 0.3643
## Anaerotignum_sp_MSJ_24 Bittarella_massiliensis Blautia_SGB4815
## Min. :-4.3845 Min. :-5.2521 Min. :-5.8095
## 1st Qu.:-1.0088 1st Qu.: 0.0000 1st Qu.:-1.8332
## Median : 0.0000 Median : 0.0000 Median :-0.1304
## Mean :-0.5936 Mean :-0.6922 Mean :-1.0063
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 0.4821 Max. : 0.0000 Max. : 1.5363
## Blautia_luti Blautia_sp_OF03_15BH Butyricimonas_paravirosa
## Min. :-5.9243 Min. :-5.48886 Min. :-6.0500
## 1st Qu.:-0.8782 1st Qu.:-1.16625 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.00000 Median : 0.0000
## Mean :-0.6830 Mean :-0.75686 Mean :-0.3684
## 3rd Qu.: 0.0000 3rd Qu.: 0.00000 3rd Qu.: 0.0000
## Max. : 2.9218 Max. : 0.08327 Max. : 1.8108
## Catenibacillus_scindens Clostridiaceae_bacterium_Marseille_Q4149
## Min. :-7.0889 Min. :-5.0521
## 1st Qu.: 0.0000 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000
## Mean :-0.5142 Mean : 0.3234
## 3rd Qu.: 0.0000 3rd Qu.: 0.1292
## Max. : 0.0000 Max. : 5.7042
## Clostridium_SGB6173 Clostridium_SGB6179 Clostridium_sp_Marseille_P3244
## Min. :-6.083 Min. :-5.078 Min. :-6.9192
## 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.0000
## Median : 0.000 Median : 0.000 Median : 0.0000
## Mean :-0.327 Mean :-0.309 Mean :-0.6426
## 3rd Qu.: 0.000 3rd Qu.: 0.000 3rd Qu.: 0.0000
## Max. : 3.230 Max. : 3.402 Max. : 0.0000
## Clostridium_sp_NSJ_42 Coprobacter_secundus Eubacteriaceae_bacterium
## Min. :-5.7599 Min. :-6.2571 Min. :-5.8953
## 1st Qu.: 0.0000 1st Qu.:-0.6748 1st Qu.:-1.5891
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.2637 Mean :-0.6056 Mean :-0.6869
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 3.4751 Max. : 1.4822 Max. : 5.2795
## Faecalibacillus_faecis Faecalibacillus_intestinalis GGB13489_SGB15224
## Min. :-5.0189 Min. :-5.9421 Min. :-3.3026
## 1st Qu.: 0.0000 1st Qu.:-0.1373 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.4155 Mean :-0.1286 Mean : 0.2069
## 3rd Qu.: 0.0000 3rd Qu.: 0.7427 3rd Qu.: 0.2068
## Max. : 2.6455 Max. : 3.0314 Max. : 3.0282
## GGB2970_SGB3952 GGB3352_SGB4436 GGB34797_SGB14322 GGB34900_SGB14891
## Min. :-2.8095 Min. :-5.96473 Min. :-3.241 Min. :-6.2276
## 1st Qu.: 0.0000 1st Qu.: 0.00000 1st Qu.: 0.000 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.00000 Median : 0.000 Median : 0.0000
## Mean :-0.2337 Mean :-0.48520 Mean :-0.141 Mean :-0.6567
## 3rd Qu.: 0.0000 3rd Qu.: 0.00000 3rd Qu.: 0.000 3rd Qu.: 0.0000
## Max. : 1.3542 Max. : 0.09886 Max. : 2.295 Max. : 0.0000
## GGB3653_SGB4964 GGB4456_SGB6141 GGB4552_SGB6276 GGB51441_SGB71759
## Min. :-5.452216 Min. :-6.2652 Min. :-7.1084 Min. :-5.945
## 1st Qu.: 0.000000 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.:-1.928
## Median : 0.000000 Median : 0.0000 Median : 0.0000 Median :-0.549
## Mean :-0.084483 Mean :-0.4249 Mean : 0.3139 Mean :-1.008
## 3rd Qu.: 0.007261 3rd Qu.: 0.0000 3rd Qu.: 0.6365 3rd Qu.: 0.000
## Max. : 2.658404 Max. : 0.9505 Max. : 4.5068 Max. : 2.068
## GGB58158_SGB79798 GGB9365_SGB14341 GGB9412_SGB14770 GGB9627_SGB15081
## Min. :-7.326 Min. :-3.9307 Min. :-4.9282 Min. :-4.0878
## 1st Qu.:-2.388 1st Qu.:-0.4118 1st Qu.: 0.0000 1st Qu.: 0.0000
## Median : 0.000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-1.124 Mean :-0.4366 Mean :-0.1863 Mean : 0.3138
## 3rd Qu.: 0.000 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.6756
## Max. : 0.000 Max. : 2.8745 Max. : 2.7674 Max. : 3.2518
## GGB9712_SGB15244 GGB9747_SGB15356 GGB9767_SGB15385 GGB9787_SGB15410
## Min. :-5.0027 Min. :-5.8601 Min. :-4.9249 Min. :-6.2847
## 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.0000 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.3142 Mean : 0.6813 Mean :-0.1288 Mean :-0.4331
## 3rd Qu.: 0.0000 3rd Qu.: 1.7292 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 4.5076 Max. : 5.1183 Max. : 2.6607 Max. : 1.3411
## GGB9790_SGB15413 Haemophilus_parainfluenzae Intestinibacter_bartlettii
## Min. :-5.2667 Min. :-4.4106 Min. :-5.0906
## 1st Qu.: 0.0000 1st Qu.:-1.7155 1st Qu.:-0.5591
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.2979 Mean :-0.8484 Mean :-0.4847
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 1.5817 Max. : 1.2033 Max. : 1.8226
## Lachnospira_sp_NSJ_43 Lachnospiraceae_bacterium_OM04_12BH Lactococcus_lactis
## Min. :-4.2193 Min. :-5.8053 Min. :-4.1685
## 1st Qu.: 0.0000 1st Qu.:-0.7840 1st Qu.: 0.0000
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean : 0.3480 Mean :-0.6651 Mean :-0.1791
## 3rd Qu.: 0.9412 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 4.6982 Max. : 2.6057 Max. : 2.2243
## Lentihominibacter_faecis Massilioclostridium_coli
## Min. :-6.0609 Min. :-7.2232
## 1st Qu.:-1.6673 1st Qu.:-0.9072
## Median : 0.0000 Median : 0.0000
## Mean :-0.9779 Mean :-0.7921
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 2.0767 Max. : 0.8236
## Mediterraneibacter_butyricigenes Mediterraneibacter_sp_NSJ_151
## Min. :-6.744 Min. :-4.2915
## 1st Qu.:-2.882 1st Qu.: 0.0000
## Median :-1.285 Median : 0.0000
## Mean :-1.584 Mean :-0.3781
## 3rd Qu.: 0.000 3rd Qu.: 0.0000
## Max. : 0.000 Max. : 0.0000
## Methanobrevibacter_smithii Romboutsia_timonensis Ruminococcus_gnavus
## Min. :-5.15172 Min. :-5.6214 Min. :-6.2707
## 1st Qu.: 0.00000 1st Qu.:-0.5506 1st Qu.:-1.6294
## Median : 0.00000 Median : 0.0000 Median : 0.0000
## Mean : 0.09254 Mean :-0.3860 Mean :-0.8162
## 3rd Qu.: 0.00000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 6.45727 Max. : 3.1234 Max. : 4.5988
## Ruminococcus_lactaris Ruminococcus_sp_AF41_9 Senegalimassilia_anaerobia
## Min. :-5.75627 Min. :-5.3581 Min. :-4.6477
## 1st Qu.: 0.00000 1st Qu.: 0.0000 1st Qu.:-0.5257
## Median : 0.00000 Median : 0.0000 Median : 0.0000
## Mean :-0.01148 Mean :-0.2957 Mean :-0.3788
## 3rd Qu.: 0.38389 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 3.36317 Max. : 2.5332 Max. : 1.5076
## Slackia_isoflavoniconvertens Streptococcus_parasanguinis Veillonella_dispar
## Min. :-2.91078 Min. :-6.2756 Min. :-6.2739
## 1st Qu.: 0.00000 1st Qu.:-2.1707 1st Qu.:-1.1894
## Median : 0.00000 Median : 0.0000 Median : 0.0000
## Mean : 0.03323 Mean :-1.1185 Mean :-0.7324
## 3rd Qu.: 0.00000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 2.60620 Max. : 0.9195 Max. : 1.5623
## Victivallis_lenta Bifidobacterium_pseudocatenulatum Eubacterium_sp_AF34_35BH
## Min. :-5.6533 Min. :-4.831605 Min. :-5.2777
## 1st Qu.: 0.0000 1st Qu.: 0.000000 1st Qu.:-0.1684
## Median : 0.0000 Median : 0.000000 Median : 0.0000
## Mean : 0.1367 Mean :-0.000609 Mean :-0.3399
## 3rd Qu.: 0.0000 3rd Qu.: 0.000000 3rd Qu.: 0.0000
## Max. : 3.5130 Max. : 3.718131 Max. : 1.3687
## Faecalicatena_contorta GGB9559_SGB14969 GGB9759_SGB15370 Roseburia_lenta
## Min. :-6.9017 Min. :-5.6428 Min. :-4.7775 Min. :-3.11486
## 1st Qu.: 0.0000 1st Qu.:-1.0706 1st Qu.: 0.0000 1st Qu.: 0.00000
## Median : 0.0000 Median : 0.0000 Median : 0.0000 Median : 0.00000
## Mean :-0.6991 Mean :-0.7472 Mean :-0.1596 Mean : 0.28856
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.02958
## Max. : 0.0000 Max. : 0.8908 Max. : 2.1550 Max. : 4.02433
## Enterocloster_bolteae GGB2848_SGB3813 GGB3005_SGB3996 GGB3061_SGB4063
## Min. :-5.530 Min. :-6.469 Min. :-6.4363 Min. :-5.2983
## 1st Qu.:-1.858 1st Qu.:-2.216 1st Qu.:-1.1200 1st Qu.: 0.0000
## Median : 0.000 Median : 0.000 Median : 0.0000 Median : 0.0000
## Mean :-1.046 Mean :-1.072 Mean :-0.7651 Mean :-0.3932
## 3rd Qu.: 0.000 3rd Qu.: 0.000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 1.563 Max. : 1.288 Max. : 1.0962 Max. : 0.9089
## GGB36331_SGB15121 Hungatella_hathewayi TM7_phylum_sp_oral_taxon_352
## Min. :-5.6253 Min. :-6.4091 Min. :-4.6915
## 1st Qu.: 0.0000 1st Qu.:-1.4589 1st Qu.:-2.3671
## Median : 0.0000 Median : 0.0000 Median : 0.0000
## Mean :-0.1716 Mean :-0.8347 Mean :-1.2015
## 3rd Qu.: 0.0000 3rd Qu.: 0.0000 3rd Qu.: 0.0000
## Max. : 1.8458 Max. : 4.7239 Max. : 0.9325
## Veillonella_parvula GGB6649_SGB9391 Veillonella_atypica
## Min. :-5.8684 Min. :-4.504849 Min. :-5.6143
## 1st Qu.:-1.6149 1st Qu.: 0.000000 1st Qu.:-1.1989
## Median : 0.0000 Median : 0.000000 Median : 0.0000
## Mean :-0.8513 Mean : 0.006198 Mean :-0.6422
## 3rd Qu.: 0.0000 3rd Qu.: 0.062313 3rd Qu.: 0.0000
## Max. : 2.3069 Max. : 2.259711 Max. : 1.66583.2.1.1 Distributions - clr transformed
Open code
check <- data_microbiome_original %>%
dplyr::select(
Adlercreutzia_equolifaciens:Veillonella_atypica
) %>%
na.omit()
size = c(8, 7)
par(mfrow = c(size[1],size[2]))
par(mar=c(2,1.5,2,0.5))
set.seed(16)
ran <- sample(1:ncol(check), size[1]*size[2], replace = FALSE)
for(x in ran){
hist(check[,x],
16,
col='blue',
main = paste0(colnames(check)[x])
)
}
3.2.1.2 Comparison training vs validation cohort
Open code
check <- data_merged %>% select(-Data, -Diet)
size = c(8,7)
ran <- sample(1:ncol(check), size[1]*size[2], replace = FALSE)
par(mfrow = c(size[1],size[2]))
par(mar = c(2,1.5,2,0.5))
par(mgp = c(3, 0.5, 0 ))
for(x in ran){
plot(
data_merged[, x+2] ~ factor(data_merged$Data),
main = paste0(colnames(check)[x])
)
}
3.2.1.3 Metabolites accross groups
Open code
colo <- c('#329243', '#F9FFAF')
data_merged <- na.omit(data_merged)
outcomes <- common_microbiome[
sample(
1:length(common_microbiome), 35, replace = FALSE
)
]
boxplot_cond <- function(variable) {
p <- ggboxplot(data_merged,
x = 'Diet',
y = variable,
fill = 'Diet',
tip.length = 0.15,
palette = colo,
outlier.shape = 1,
lwd = 0.25,
outlier.size = 0.8,
facet.by = 'Data',
title = variable,
ylab = 'Lipid level') +
theme(
plot.title = element_text(size = 10),
axis.title = element_text(size = 8),
axis.text.y = element_text(size = 7),
axis.text.x = element_blank(),
axis.title.x = element_blank()
)
return(p)
}
# Plot all outcomes
plots <- map(outcomes, boxplot_cond)
# Create a matrix of plots
plots_arranged <- ggarrange(plotlist = plots, ncol = 5, nrow = 7, common.legend = TRUE)
plots_arranged
4 Linear models across taxa
We will fit a feature-specific linear model where the CLR-transformed count of bacteria reads represents the outcome variable whereas country (Italy vs Czech), diet (vegan vs omnivore), and their interaction (country:diet) all represent fixed-effects predictors. So, each model has the following form
\[ CLR({N_i}) = \alpha + \beta_{1} \times country + \beta_{2} \times diet + \beta_{3} \times country:diet + \epsilon \] where \(N_i\) is read count of \(i\)-th bacteria taxa
The variables were coded as follows: \(diet = -0.5\) for omnivores and \(diet = 0.5\) for vegans; \(country = -0.5\) for the Czech cohort and \(country = 0.5\) for the Italian cohort.
This parameterization allows us to interpret the linear model summary output as presenting the conditional effects of diet averaged across both countries and the conditional effects of country averaged across both diet groups. We will then use the emmeans package (Lenth 2024) to obtain specific estimates for the effect of diet in the Italian and Czech cohorts separately, still from a single model.
Taxa that will show a significant diet effect (average effect of diet across both countries, adjusted for multiple comparisons with FDR < 0.1) will be then visualized using a forest plot, with country-specific diet effect along with diet effect based on independent validation cohort, to evaluate how generalizable these findings are (see external validation section).
Note that p-value for avg effects are the same as produced with car::Anova(model, type = 'III').
4.1 Select data
Open code
data_analysis <- data_microbiome_original %>%
na.omit() %>%
dplyr::mutate(
Diet_VEGAN = as.numeric(
dplyr::if_else(
Diet == "VEGAN", 0.5, -0.5
)
),
Country_IT = as.numeric(
dplyr::if_else(
Country == "IT", 0.5, -0.5
)
)
) %>%
dplyr::select(
Sample,
Country,
Country_IT,
Diet,
Diet_VEGAN,
dplyr::everything()
)
summary(data_analysis[ , 1:12])
## Sample Country Country_IT Diet
## Length:166 Length:166 Min. :-0.50000 Length:166
## Class :character Class :character 1st Qu.:-0.50000 Class :character
## Mode :character Mode :character Median :-0.50000 Mode :character
## Mean :-0.03012
## 3rd Qu.: 0.50000
## Max. : 0.50000
## Diet_VEGAN Adlercreutzia_equolifaciens Agathobaculum_butyriciproducens
## Min. :-0.50000 Min. :-5.3879 Min. :-1.6741
## 1st Qu.:-0.50000 1st Qu.:-1.8236 1st Qu.: 0.9966
## Median : 0.50000 Median :-0.3954 Median : 1.7080
## Mean : 0.08434 Mean :-0.9361 Mean : 1.6332
## 3rd Qu.: 0.50000 3rd Qu.: 0.0000 3rd Qu.: 2.3623
## Max. : 0.50000 Max. : 2.9097 Max. : 4.1360
## Akkermansia_muciniphila Alistipes_communis Alistipes_finegoldii
## Min. :-5.961 Min. :-4.579 Min. :-5.9534
## 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.0000
## Median : 1.018 Median : 1.911 Median : 0.4529
## Mean : 1.437 Mean : 1.666 Mean : 0.8876
## 3rd Qu.: 3.155 3rd Qu.: 2.925 3rd Qu.: 2.0030
## Max. : 7.112 Max. : 5.808 Max. : 5.2364
## Alistipes_ihumii Alistipes_indistinctus
## Min. :-4.4586 Min. :-5.34668
## 1st Qu.: 0.0000 1st Qu.:-0.46130
## Median : 0.1777 Median : 0.00000
## Mean : 0.8382 Mean :-0.05192
## 3rd Qu.: 1.8759 3rd Qu.: 0.60784
## Max. : 4.4281 Max. : 3.545694.1.1 Define number of microbiome and covariates
Open code
n_covarites <- 5
n_features <- ncol(data_analysis) - n_covarites4.1.2 Create empty objects
Open code
outcome <- vector('double', n_features)
logFD_VGdiet_inCZ <- vector('double', n_features)
logFD_VGdiet_inIT <- vector('double', n_features)
logFD_VGdiet_avg <- vector('double', n_features)
logFD_ITcountry_avg <- vector('double', n_features)
diet_country_int <- vector('double', n_features)
P_VGdiet_inCZ <- vector('double', n_features)
P_VGdiet_inIT <- vector('double', n_features)
P_VGdiet_avg <- vector('double', n_features)
P_ITcountry_avg <- vector('double', n_features)
P_diet_country_int <- vector('double', n_features)
CI_L_VGdiet_inCZ <- vector('double', n_features)
CI_L_VGdiet_inIT <- vector('double', n_features)
CI_L_VGdiet_avg <- vector('double', n_features)
CI_U_VGdiet_inCZ <- vector('double', n_features)
CI_U_VGdiet_inIT <- vector('double', n_features)
CI_U_VGdiet_avg <- vector('double', n_features)4.1.3 Estimate over outcomes
Open code
for (i in 1:n_features) {
## define variable
data_analysis$outcome <- data_analysis[, (i + n_covarites)]
## fit model
model <- lm(outcome ~ Country_IT * Diet_VEGAN, data = data_analysis)
## get contrast (effects of diet BY COUNTRY)
contrast_emm <- summary(
pairs(
emmeans(
model,
specs = ~ Diet_VEGAN | Country_IT
),
interaction = TRUE,
adjust = "none"
),
infer = c(TRUE, TRUE)
)
## save results
outcome[i] <- names(data_analysis)[i + n_covarites]
## country effect
logFD_ITcountry_avg[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Country_IT"
), 1
]
P_ITcountry_avg[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Country_IT"
), 4
]
## diet effect
tr <- confint(model)
CI_L_VGdiet_avg[i] <- tr[which(row.names(tr) == 'Diet_VEGAN'),][1]
CI_U_VGdiet_avg[i] <- tr[which(row.names(tr) == 'Diet_VEGAN'),][2]
logFD_VGdiet_avg[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Diet_VEGAN"
), 1
]
P_VGdiet_avg[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Diet_VEGAN"
), 4
]
logFD_VGdiet_inCZ[i] <- -contrast_emm[1,3]
P_VGdiet_inCZ[i] <- contrast_emm$p.value[1]
CI_L_VGdiet_inCZ[i] <- -contrast_emm$upper.CL[1]
CI_U_VGdiet_inCZ[i] <- -contrast_emm$lower.CL[1]
logFD_VGdiet_inIT[i] <- -contrast_emm[2,3]
P_VGdiet_inIT[i] <- contrast_emm$p.value[2]
CI_L_VGdiet_inIT[i] <- -contrast_emm$upper.CL[2]
CI_U_VGdiet_inIT[i] <- -contrast_emm$lower.CL[2]
## interaction
diet_country_int[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Country_IT:Diet_VEGAN"
), 1
]
P_diet_country_int[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Country_IT:Diet_VEGAN"
), 4
]
}4.1.4 Results table
Open code
result_microbiome <- data.frame(
outcome,
logFD_ITcountry_avg, P_ITcountry_avg,
logFD_VGdiet_avg, P_VGdiet_avg,
logFD_VGdiet_inCZ, P_VGdiet_inCZ,
logFD_VGdiet_inIT, P_VGdiet_inIT,
diet_country_int, P_diet_country_int,
CI_L_VGdiet_avg, CI_U_VGdiet_avg,
CI_L_VGdiet_inCZ, CI_U_VGdiet_inCZ,
CI_L_VGdiet_inIT, CI_U_VGdiet_inIT
)4.1.5 Adjust p values
Open code
result_microbiome <- result_microbiome %>%
dplyr::mutate(
fdr_ITcountry_avg = p.adjust(P_ITcountry_avg, method = 'BH'),
fdr_VGdiet_avg = p.adjust(P_VGdiet_avg, method = 'BH'),
fdr_VGdiet_inCZ = p.adjust(P_VGdiet_inCZ, method = 'BH'),
fdr_VGdiet_inIT = p.adjust(P_VGdiet_inIT, method = 'BH'),
fdr_diet_country_int = p.adjust(P_diet_country_int, method = 'BH')
) %>%
dplyr::select(
outcome,
logFD_ITcountry_avg, P_ITcountry_avg, fdr_ITcountry_avg,
logFD_VGdiet_avg, P_VGdiet_avg, fdr_VGdiet_avg,
logFD_VGdiet_inCZ, P_VGdiet_inCZ, fdr_VGdiet_inCZ,
logFD_VGdiet_inIT, P_VGdiet_inIT, fdr_VGdiet_inIT,
diet_country_int, P_diet_country_int, fdr_diet_country_int,
CI_L_VGdiet_avg, CI_U_VGdiet_avg,
CI_L_VGdiet_inCZ, CI_U_VGdiet_inCZ,
CI_L_VGdiet_inIT, CI_U_VGdiet_inIT
)4.1.6 Show and save results
Open code
kableExtra::kable(result_microbiome,
caption = "Result of linear models, modelling the CLR-transformed reads count of given bacterial taxa, with `Diet`, `Country` and `Diet:Country` interaction as predictors. `logFD` prefix: implies estimated effects (regression coefficient), i.e. how much CLR-transformed reads count differ in vegans compared to omnivores, `P`: p-value, `fdr`: p-value after adjustment for multiple comparison, `CI_L` and `CI_U`: lower and upper bounds of 95% confidence interval respectively. `avg` suffix shows effect averaged across subgroups, whereas `inCZ` and `inIT` shows effect in Czech or Italian cohort respectively. All estimates in a single row are based on a single model"
)| outcome | logFD_ITcountry_avg | P_ITcountry_avg | fdr_ITcountry_avg | logFD_VGdiet_avg | P_VGdiet_avg | fdr_VGdiet_avg | logFD_VGdiet_inCZ | P_VGdiet_inCZ | fdr_VGdiet_inCZ | logFD_VGdiet_inIT | P_VGdiet_inIT | fdr_VGdiet_inIT | diet_country_int | P_diet_country_int | fdr_diet_country_int | CI_L_VGdiet_avg | CI_U_VGdiet_avg | CI_L_VGdiet_inCZ | CI_U_VGdiet_inCZ | CI_L_VGdiet_inIT | CI_U_VGdiet_inIT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Adlercreutzia_equolifaciens | -0.0614960 | 0.7942844 | 0.8642788 | -0.3036485 | 0.1990160 | 0.5056979 | -0.7568838 | 0.0244163 | 0.1839238 | 0.1495869 | 0.6536796 | 0.9931883 | 0.9064707 | 0.0559880 | 0.5300197 | -0.7686018 | 0.1613048 | -1.4147986 | -0.0989691 | -0.5075848 | 0.8067585 |
| Agathobaculum_butyriciproducens | 0.5346760 | 0.0005963 | 0.0020908 | 0.8279723 | 0.0000002 | 0.0000594 | 0.9144912 | 0.0000385 | 0.0036425 | 0.7414533 | 0.0007497 | 0.0831380 | -0.1730379 | 0.5716885 | 0.9826710 | 0.5265003 | 1.1294442 | 0.4879047 | 1.3410778 | 0.3153486 | 1.1675580 |
| Akkermansia_muciniphila | 0.2265332 | 0.5346338 | 0.6548793 | 0.4426396 | 0.2257864 | 0.5213278 | 0.2448765 | 0.6351576 | 0.8589750 | 0.6404028 | 0.2150693 | 0.7316337 | 0.3955263 | 0.5877058 | 0.9826710 | -0.2762329 | 1.1615122 | -0.7723372 | 1.2620901 | -0.3756618 | 1.6564675 |
| Alistipes_communis | 1.4156089 | 0.0000002 | 0.0000022 | -0.1459676 | 0.5792885 | 0.8025543 | 0.1392988 | 0.7083954 | 0.8924991 | -0.4312340 | 0.2472697 | 0.7493886 | -0.5705328 | 0.2792210 | 0.8436038 | -0.6648179 | 0.3728827 | -0.5948808 | 0.8734784 | -1.1645844 | 0.3021163 |
| Alistipes_finegoldii | 1.5797872 | 0.0000000 | 0.0000003 | 0.0867226 | 0.7491813 | 0.8861676 | -0.3083441 | 0.4221546 | 0.7400735 | 0.4817892 | 0.2099072 | 0.7316337 | 0.7901333 | 0.1465103 | 0.6639826 | -0.4480011 | 0.6214462 | -1.0649847 | 0.4482966 | -0.2739968 | 1.2375752 |
| Alistipes_ihumii | 0.8177299 | 0.0005524 | 0.0020114 | 0.0088453 | 0.9696389 | 0.9834909 | 0.0171960 | 0.9582959 | 0.9973905 | 0.0004946 | 0.9987986 | 1.0000000 | -0.0167014 | 0.9713358 | 0.9948202 | -0.4493627 | 0.4670533 | -0.6311741 | 0.6655660 | -0.6471431 | 0.6481323 |
| Alistipes_indistinctus | 0.5482124 | 0.0204565 | 0.0489740 | -0.1199680 | 0.6091625 | 0.8084213 | -0.2452204 | 0.4603765 | 0.7709511 | 0.0052844 | 0.9872824 | 1.0000000 | 0.2505047 | 0.5935005 | 0.9826710 | -0.5824283 | 0.3424923 | -0.8996075 | 0.4091667 | -0.6483636 | 0.6589323 |
| Alistipes_onderdonkii | 1.1563653 | 0.0023953 | 0.0073941 | -0.3258552 | 0.3859757 | 0.7078181 | 0.1297417 | 0.8070748 | 0.9471457 | -0.7814522 | 0.1421716 | 0.6749058 | -0.9111939 | 0.2259812 | 0.7792030 | -1.0660834 | 0.4143729 | -0.9176903 | 1.1771738 | -1.8277011 | 0.2647967 |
| Alistipes_putredinis | 0.9445127 | 0.0282302 | 0.0626357 | -0.8463122 | 0.0489734 | 0.3082348 | -0.7962487 | 0.1890307 | 0.5389703 | -0.8963757 | 0.1390798 | 0.6749058 | -0.1001269 | 0.9067293 | 0.9826710 | -1.6887706 | -0.0038538 | -1.9883379 | 0.3958404 | -2.0871183 | 0.2943670 |
| Alistipes_senegalensis | 0.9322196 | 0.0000170 | 0.0000945 | 0.1316225 | 0.5321203 | 0.7830163 | -0.1766143 | 0.5535200 | 0.8080869 | 0.4398594 | 0.1407181 | 0.6749058 | 0.6164737 | 0.1445178 | 0.6639826 | -0.2835038 | 0.5467489 | -0.7640232 | 0.4107946 | -0.1468861 | 1.0266048 |
| Alistipes_shahii | 1.4174456 | 0.0000021 | 0.0000148 | 0.1891343 | 0.5126785 | 0.7827994 | 0.2018996 | 0.6212851 | 0.8482931 | 0.1763690 | 0.6656796 | 0.9931883 | -0.0255307 | 0.9647328 | 0.9948202 | -0.3801017 | 0.7583703 | -0.6035765 | 1.0073757 | -0.6281973 | 0.9809352 |
| Anaerobutyricum_hallii | -1.8955964 | 0.0000000 | 0.0000000 | -0.4257955 | 0.0499254 | 0.3082348 | -0.5754616 | 0.0609899 | 0.3093058 | -0.2761295 | 0.3661031 | 0.8507175 | 0.2993320 | 0.4884658 | 0.9826710 | -0.8514507 | -0.0001404 | -1.1777689 | 0.0268457 | -0.8777565 | 0.3254975 |
| Anaerofilum_hominis | -0.0089662 | 0.9737315 | 0.9806374 | 0.7155077 | 0.0093145 | 0.1151234 | 0.8841607 | 0.0228227 | 0.1839238 | 0.5468547 | 0.1566262 | 0.6950289 | -0.3373060 | 0.5359045 | 0.9826710 | 0.1786396 | 1.2523758 | 0.1244856 | 1.6438358 | -0.2119623 | 1.3056717 |
| Anaeromassilibacillus_senegalensis | 0.2107823 | 0.4104327 | 0.5429330 | 0.0351464 | 0.8907214 | 0.9582003 | 0.3295059 | 0.3632679 | 0.6934416 | -0.2592130 | 0.4737669 | 0.9749986 | -0.5887189 | 0.2508154 | 0.8073470 | -0.4692168 | 0.5395096 | -0.3841743 | 1.0431861 | -0.9720871 | 0.4536611 |
| Anaerostipes_hadrus | -2.9248630 | 0.0000000 | 0.0000000 | 0.2033639 | 0.4001773 | 0.7078181 | -0.2058624 | 0.5470525 | 0.8080869 | 0.6125902 | 0.0740811 | 0.6187951 | 0.8184526 | 0.0915378 | 0.5878263 | -0.2727152 | 0.6794430 | -0.8795203 | 0.4677955 | -0.0603068 | 1.2854872 |
| Anaerotignum_faecicola | -0.7584214 | 0.0005088 | 0.0019012 | -0.7661305 | 0.0004479 | 0.0198577 | -1.1130716 | 0.0003178 | 0.0152257 | -0.4191894 | 0.1672638 | 0.6963755 | 0.6938822 | 0.1065669 | 0.6176528 | -1.1882964 | -0.3439645 | -1.7104417 | -0.5157015 | -1.0158847 | 0.1775060 |
| Anaerotruncus_colihominis | 0.0303582 | 0.8906679 | 0.9231740 | 0.4729027 | 0.0334735 | 0.2532106 | 0.3081960 | 0.3247486 | 0.6856880 | 0.6376095 | 0.0423922 | 0.4815749 | 0.3294135 | 0.4561767 | 0.9815046 | 0.0374663 | 0.9083392 | -0.3079520 | 0.9243439 | 0.0221575 | 1.2530615 |
| Anaerotruncus_massiliensis | -0.3888396 | 0.0643297 | 0.1251344 | 0.2080020 | 0.3205611 | 0.6553058 | 0.4352922 | 0.1425392 | 0.4616646 | -0.0192881 | 0.9479613 | 1.0000000 | -0.4545802 | 0.2778800 | 0.8436038 | -0.2042434 | 0.6202475 | -0.1480403 | 1.0186246 | -0.6019617 | 0.5633855 |
| Anaerotruncus_rubiinfantis | 0.4760658 | 0.0385038 | 0.0810006 | -0.0114854 | 0.9599156 | 0.9832997 | 0.1040057 | 0.7477649 | 0.9153674 | -0.1269766 | 0.6942994 | 0.9931883 | -0.2309823 | 0.6134297 | 0.9826710 | -0.4620554 | 0.4390846 | -0.5335564 | 0.7415679 | -0.7638186 | 0.5098654 |
| Bacteroides_caccae | -0.3561368 | 0.1462696 | 0.2371081 | -0.3651931 | 0.1363479 | 0.4665397 | -0.5059492 | 0.1446766 | 0.4616646 | -0.2244370 | 0.5160331 | 0.9931883 | 0.2815122 | 0.5647575 | 0.9826710 | -0.8469359 | 0.1165497 | -1.1876213 | 0.1757228 | -0.9053391 | 0.4564651 |
| Bacteroides_cellulosilyticus | -0.4363713 | 0.1264674 | 0.2088183 | 0.1506300 | 0.5966722 | 0.8025543 | 0.2192981 | 0.5861255 | 0.8281574 | 0.0819619 | 0.8385096 | 1.0000000 | -0.1373362 | 0.8093017 | 0.9826710 | -0.4103462 | 0.7116063 | -0.5744903 | 1.0130866 | -0.7109299 | 0.8748538 |
| Bacteroides_clarus | -0.2274338 | 0.4041730 | 0.5412435 | 0.1653956 | 0.5438823 | 0.7844941 | -0.1587345 | 0.6804936 | 0.8835689 | 0.4895257 | 0.2046070 | 0.7316337 | 0.6482602 | 0.2350133 | 0.7852210 | -0.3715817 | 0.7023729 | -0.9185640 | 0.6010951 | -0.2694456 | 1.2484970 |
| Bacteroides_eggerthii | 0.1342165 | 0.7043028 | 0.8065403 | -0.2632158 | 0.4569892 | 0.7397360 | -0.2007339 | 0.6883303 | 0.8835689 | -0.3256977 | 0.5148498 | 0.9931883 | -0.1249638 | 0.8597374 | 0.9826710 | -0.9603402 | 0.4339086 | -1.1871736 | 0.7857058 | -1.3110232 | 0.6596278 |
| Bacteroides_fragilis | -0.0442056 | 0.8253848 | 0.8746372 | 0.0587498 | 0.7693722 | 0.8861676 | -0.1164111 | 0.6814272 | 0.8835689 | 0.2339106 | 0.4092868 | 0.8873087 | 0.3503217 | 0.3825316 | 0.9699910 | -0.3362753 | 0.4537748 | -0.6753764 | 0.4425543 | -0.3244234 | 0.7922446 |
| Bacteroides_ovatus | -0.8483739 | 0.0040157 | 0.0120047 | 0.4946195 | 0.0907409 | 0.3878452 | 0.3770543 | 0.3606477 | 0.6934416 | 0.6121847 | 0.1381472 | 0.6749058 | 0.2351303 | 0.6864079 | 0.9826710 | -0.0793748 | 1.0686138 | -0.4351548 | 1.1892635 | -0.1991071 | 1.4234764 |
| Bacteroides_stercoris | -0.5632263 | 0.1575283 | 0.2527573 | -0.1341134 | 0.7357061 | 0.8779013 | -0.2682435 | 0.6333357 | 0.8589750 | 0.0000167 | 0.9999762 | 1.0000000 | 0.2682602 | 0.7356743 | 0.9826710 | -0.9173595 | 0.6491327 | -1.3765465 | 0.8400595 | -1.1070344 | 1.1070679 |
| Bacteroides_thetaiotaomicron | -1.0299489 | 0.0004577 | 0.0017333 | -0.0489703 | 0.8651458 | 0.9560366 | -0.1904539 | 0.6407608 | 0.8624459 | 0.0925133 | 0.8204366 | 1.0000000 | 0.2829672 | 0.6237804 | 0.9826710 | -0.6174830 | 0.5195424 | -0.9949065 | 0.6139986 | -0.7110306 | 0.8960572 |
| Bacteroides_uniformis | 0.3455271 | 0.2172031 | 0.3270814 | -0.0748054 | 0.7888861 | 0.8998423 | 0.0128016 | 0.9741641 | 0.9973905 | -0.1624123 | 0.6808984 | 0.9931883 | -0.1752139 | 0.7538505 | 0.9826710 | -0.6255846 | 0.4759739 | -0.7665579 | 0.7921611 | -0.9408915 | 0.6160668 |
| Bacteroides_xylanisolvens | -0.7462881 | 0.0039621 | 0.0119705 | 0.0278735 | 0.9131985 | 0.9605496 | -0.0169806 | 0.9625687 | 0.9973905 | 0.0727275 | 0.8405286 | 1.0000000 | 0.0897081 | 0.8607607 | 0.9826710 | -0.4762895 | 0.5320364 | -0.7303774 | 0.6964163 | -0.6398636 | 0.7853186 |
| Barnesiella_intestinihominis | -0.4560620 | 0.0482146 | 0.0971131 | -0.5545883 | 0.0166022 | 0.1473444 | -0.5434110 | 0.0956377 | 0.3994282 | -0.5657657 | 0.0825192 | 0.6333906 | -0.0223547 | 0.9611509 | 0.9948202 | -1.0070272 | -0.1021494 | -1.1836176 | 0.0967957 | -1.2052493 | 0.0737179 |
| Bifidobacterium_adolescentis | -0.6155977 | 0.0680443 | 0.1280893 | -0.2758952 | 0.4115531 | 0.7078181 | -0.4756708 | 0.3172963 | 0.6856880 | -0.0761196 | 0.8725241 | 1.0000000 | 0.3995512 | 0.5519108 | 0.9826710 | -0.9376476 | 0.3858573 | -1.4120588 | 0.4607172 | -1.0114499 | 0.8592107 |
| Bifidobacterium_longum | 0.6487073 | 0.0199337 | 0.0486526 | -0.3362453 | 0.2247953 | 0.5213278 | -0.0064432 | 0.9868547 | 0.9973905 | -0.6660473 | 0.0896054 | 0.6432181 | -0.6596041 | 0.2337645 | 0.7852210 | -0.8811564 | 0.2086658 | -0.7774993 | 0.7646128 | -1.4362324 | 0.1041378 |
| Bilophila_SGB15451 | -0.7056271 | 0.0001804 | 0.0008007 | -0.1597682 | 0.3866757 | 0.7078181 | -0.0529905 | 0.8390344 | 0.9608298 | -0.2665460 | 0.3071016 | 0.8001546 | -0.2135555 | 0.5626444 | 0.9826710 | -0.5232419 | 0.2037054 | -0.5673102 | 0.4613292 | -0.7802848 | 0.2471928 |
| Bilophila_wadsworthia | 1.3934528 | 0.0000000 | 0.0000002 | -0.3725428 | 0.1129984 | 0.4222573 | -0.4032276 | 0.2246579 | 0.5853472 | -0.3418580 | 0.3024218 | 0.8001546 | 0.0613696 | 0.8957408 | 0.9826710 | -0.8342112 | 0.0891256 | -1.0564942 | 0.2500389 | -0.9943867 | 0.3106706 |
| Blautia_faecis | -1.3614636 | 0.0000000 | 0.0000003 | -0.0327953 | 0.8880960 | 0.9582003 | -0.1349206 | 0.6825253 | 0.8835689 | 0.0693300 | 0.8333121 | 1.0000000 | 0.2042507 | 0.6613360 | 0.9826710 | -0.4923064 | 0.4267158 | -0.7851346 | 0.5152933 | -0.5801495 | 0.7188095 |
| Blautia_glucerasea | -0.1263392 | 0.6164955 | 0.7295197 | -0.2220832 | 0.3790482 | 0.7078181 | -0.3455219 | 0.3335715 | 0.6856880 | -0.0986445 | 0.7819821 | 1.0000000 | 0.2468774 | 0.6246052 | 0.9826710 | -0.7192698 | 0.2751033 | -1.0490471 | 0.3580033 | -0.8013750 | 0.6040860 |
| Blautia_massiliensis | -1.4162505 | 0.0000006 | 0.0000047 | -0.3821926 | 0.1625235 | 0.4843937 | -0.8764856 | 0.0242862 | 0.1839238 | 0.1121003 | 0.7713074 | 1.0000000 | 0.9885859 | 0.0714443 | 0.5797192 | -0.9201178 | 0.1557326 | -1.6376565 | -0.1153147 | -0.6482108 | 0.8724114 |
| Blautia_obeum | -1.0121044 | 0.0000166 | 0.0000941 | 0.0993463 | 0.6635318 | 0.8325810 | 0.1907875 | 0.5549992 | 0.8080869 | 0.0079052 | 0.9804546 | 1.0000000 | -0.1828824 | 0.6888303 | 0.9826710 | -0.3507731 | 0.5494658 | -0.4461371 | 0.8277122 | -0.6283001 | 0.6441104 |
| Blautia_sp_MCC283 | -0.1466664 | 0.5567174 | 0.6736447 | 0.1836045 | 0.4620223 | 0.7397360 | 0.2746780 | 0.4368299 | 0.7573466 | 0.0925310 | 0.7929744 | 1.0000000 | -0.1821470 | 0.7150581 | 0.9826710 | -0.3081622 | 0.6753712 | -0.4211780 | 0.9705341 | -0.6025391 | 0.7876011 |
| Blautia_wexlerae | -2.3493073 | 0.0000000 | 0.0000000 | -0.3448441 | 0.1521558 | 0.4779906 | -0.5729456 | 0.0930832 | 0.3945616 | -0.1167427 | 0.7308410 | 0.9931883 | 0.4562029 | 0.3426836 | 0.9442582 | -0.8181563 | 0.1284680 | -1.2426882 | 0.0967970 | -0.7857288 | 0.5522435 |
| Brotolimicola_acetigignens | 0.1353203 | 0.6545573 | 0.7649970 | 0.5759606 | 0.0581651 | 0.3339497 | 0.7695106 | 0.0734858 | 0.3448326 | 0.3824107 | 0.3714401 | 0.8507175 | -0.3870998 | 0.5223215 | 0.9826710 | -0.0201513 | 1.1720725 | -0.0739952 | 1.6130163 | -0.4601423 | 1.2249637 |
| Butyricimonas_faecihominis | 0.4003576 | 0.0197970 | 0.0486526 | 0.0633033 | 0.7102821 | 0.8620518 | 0.0849810 | 0.7245134 | 0.9024640 | 0.0416255 | 0.8627695 | 1.0000000 | -0.0433555 | 0.8987555 | 0.9826710 | -0.2726166 | 0.3992231 | -0.3903498 | 0.5603118 | -0.4331684 | 0.5164194 |
| Butyricimonas_virosa | 0.0550661 | 0.7787735 | 0.8539447 | 0.3260133 | 0.0976624 | 0.4019728 | 0.6689249 | 0.0168192 | 0.1687600 | -0.0168983 | 0.9513604 | 1.0000000 | -0.6858232 | 0.0816199 | 0.5878263 | -0.0604306 | 0.7124572 | 0.1221019 | 1.2157479 | -0.5631036 | 0.5293070 |
| Candidatus_Borkfalkia_ceftriaxoniphila | 0.1986226 | 0.2564394 | 0.3754062 | -0.0111994 | 0.9488780 | 0.9763818 | -0.0013646 | 0.9955948 | 1.0000000 | -0.0210341 | 0.9321048 | 1.0000000 | -0.0196695 | 0.9551001 | 0.9948202 | -0.3555968 | 0.3331981 | -0.4886913 | 0.4859620 | -0.5078103 | 0.4657421 |
| Candidatus_Cibionibacter_quicibialis | 1.1064434 | 0.0000178 | 0.0000973 | -0.2220064 | 0.3761915 | 0.7078181 | -0.6107258 | 0.0864062 | 0.3724833 | 0.1667130 | 0.6379484 | 0.9931883 | 0.7774388 | 0.1221975 | 0.6538840 | -0.7160463 | 0.2720335 | -1.3097984 | 0.0883468 | -0.5315700 | 0.8649960 |
| Clostridia_bacterium_UC5_1_1D1 | -0.7611670 | 0.0006880 | 0.0023829 | 0.4231452 | 0.0561005 | 0.3319281 | 0.0549157 | 0.8601472 | 0.9732343 | 0.7913747 | 0.0118326 | 0.2375212 | 0.7364590 | 0.0959907 | 0.5926385 | -0.0111411 | 0.8574315 | -0.5596049 | 0.6694362 | 0.1775482 | 1.4052011 |
| Clostridiaceae_bacterium | -1.7388199 | 0.0000000 | 0.0000000 | 0.2981331 | 0.1420141 | 0.4692485 | 0.2590470 | 0.3662544 | 0.6934416 | 0.3372193 | 0.2394117 | 0.7493886 | 0.0781723 | 0.8468528 | 0.9826710 | -0.1008643 | 0.6971305 | -0.3055394 | 0.8236333 | -0.2267293 | 0.9011679 |
| Clostridiaceae_bacterium_AF18_31LB | 0.4302731 | 0.0297953 | 0.0655959 | 0.0804644 | 0.6823850 | 0.8425971 | 0.2956365 | 0.2887107 | 0.6783679 | -0.1347076 | 0.6279307 | 0.9931883 | -0.4303441 | 0.2745940 | 0.8436038 | -0.3071311 | 0.4680599 | -0.2528160 | 0.8440890 | -0.6825406 | 0.4131254 |
| Clostridiaceae_bacterium_Marseille_Q4143 | 0.4967185 | 0.0234273 | 0.0545358 | -0.0917692 | 0.6730603 | 0.8383734 | -0.2951891 | 0.3380152 | 0.6856880 | 0.1116507 | 0.7164288 | 0.9931883 | 0.4068397 | 0.3501430 | 0.9442582 | -0.5204648 | 0.3369264 | -0.9017987 | 0.3114206 | -0.4942738 | 0.7175751 |
| Clostridiaceae_bacterium_Marseille_Q4145 | -0.1230312 | 0.5843983 | 0.7027513 | 0.0095868 | 0.9659880 | 0.9832997 | -0.0856504 | 0.7877779 | 0.9361043 | 0.1048240 | 0.7415409 | 0.9931883 | 0.1904744 | 0.6719426 | 0.9826710 | -0.4336992 | 0.4528728 | -0.7129056 | 0.5416049 | -0.5217228 | 0.7313708 |
| Clostridiales_bacterium | 1.4379104 | 0.0000000 | 0.0000000 | -0.1070684 | 0.6204678 | 0.8158003 | -0.1380774 | 0.6517483 | 0.8689977 | -0.0760593 | 0.8033985 | 1.0000000 | 0.0620182 | 0.8859223 | 0.9826710 | -0.5332170 | 0.3190803 | -0.7410831 | 0.4649282 | -0.6783838 | 0.5262653 |
| Clostridiales_bacterium_KLE1615 | -1.2833221 | 0.0000000 | 0.0000004 | -0.1689414 | 0.4449112 | 0.7303745 | -0.0054629 | 0.9860593 | 0.9973905 | -0.3324199 | 0.2879676 | 0.7788837 | -0.3269571 | 0.4597452 | 0.9815046 | -0.6045804 | 0.2666977 | -0.6218976 | 0.6109718 | -0.9481583 | 0.2833185 |
| Clostridium_SGB4750 | -1.3663630 | 0.0000000 | 0.0000001 | -0.2465903 | 0.2618133 | 0.5719615 | -0.2933415 | 0.3452246 | 0.6904493 | -0.1998391 | 0.5194270 | 0.9931883 | 0.0935024 | 0.8312157 | 0.9826710 | -0.6790305 | 0.1858500 | -0.9052499 | 0.3185669 | -0.8110563 | 0.4113782 |
| Clostridium_SGB4909 | -0.3000268 | 0.2865312 | 0.4151778 | 0.0499601 | 0.8589011 | 0.9528434 | 0.2804109 | 0.4810368 | 0.7851405 | -0.1804906 | 0.6496372 | 0.9931883 | -0.4609015 | 0.4126712 | 0.9815046 | -0.5041173 | 0.6040375 | -0.5036156 | 1.0644373 | -0.9636315 | 0.6026503 |
| Clostridium_fessum | -0.6882767 | 0.0002905 | 0.0012456 | -0.7462469 | 0.0000903 | 0.0064196 | -0.7461517 | 0.0051223 | 0.0909210 | -0.7463421 | 0.0050625 | 0.1198134 | -0.0001904 | 0.9995919 | 0.9995919 | -1.1131698 | -0.3793240 | -1.2653522 | -0.2269512 | -1.2649561 | -0.2277280 |
| Clostridium_leptum | -0.2791866 | 0.2118559 | 0.3234789 | 0.2877047 | 0.1983110 | 0.5056979 | 0.7062355 | 0.0264013 | 0.1874496 | -0.1308261 | 0.6782847 | 0.9931883 | -0.8370616 | 0.0620375 | 0.5505824 | -0.1521404 | 0.7275498 | 0.0838492 | 1.3286218 | -0.7525094 | 0.4908572 |
| Clostridium_sp_AF20_17LB | 0.7819860 | 0.0016161 | 0.0051571 | 0.4186926 | 0.0878674 | 0.3878452 | 0.5949273 | 0.0865630 | 0.3724833 | 0.2424579 | 0.4827446 | 0.9833147 | -0.3524694 | 0.4708655 | 0.9826710 | -0.0628093 | 0.9001945 | -0.0864039 | 1.2762585 | -0.4381037 | 0.9230195 |
| Clostridium_sp_AF27_2AA | -0.1956906 | 0.3219920 | 0.4516249 | 0.1962029 | 0.3207307 | 0.6553058 | 0.7511658 | 0.0077848 | 0.1196466 | -0.3587601 | 0.1994002 | 0.7316337 | -1.1099260 | 0.0054470 | 0.2087999 | -0.1927941 | 0.5851998 | 0.2007303 | 1.3016014 | -0.9085740 | 0.1910537 |
| Clostridium_sp_AF36_4 | -0.5008631 | 0.0683607 | 0.1280893 | -0.0448974 | 0.8695609 | 0.9571910 | -0.2524275 | 0.5143464 | 0.8070408 | 0.1626328 | 0.6739313 | 0.9931883 | 0.4150603 | 0.4482014 | 0.9815046 | -0.5839373 | 0.4941425 | -1.0151757 | 0.5103207 | -0.5992539 | 0.9245194 |
| Clostridium_sp_AM22_11AC | -1.4668820 | 0.0000000 | 0.0000000 | -0.1321066 | 0.5124007 | 0.7827994 | -0.0862622 | 0.7622988 | 0.9212462 | -0.1779511 | 0.5323834 | 0.9931883 | -0.0916889 | 0.8200575 | 0.9826710 | -0.5294447 | 0.2652315 | -0.6485005 | 0.4759762 | -0.7395543 | 0.3836522 |
| Clostridium_sp_AM33_3 | -0.1177008 | 0.5146238 | 0.6410226 | 0.0556913 | 0.7577065 | 0.8861676 | 0.1882424 | 0.4614848 | 0.7709511 | -0.0768598 | 0.7632421 | 0.9943154 | -0.2651022 | 0.4631043 | 0.9815046 | -0.3001947 | 0.4115772 | -0.3153407 | 0.6918254 | -0.5798740 | 0.4261544 |
| Collinsella_aerofaciens | 0.1446952 | 0.4115483 | 0.5429330 | -0.5620412 | 0.0016648 | 0.0429828 | -0.6677641 | 0.0080045 | 0.1196466 | -0.4563182 | 0.0680468 | 0.6187951 | 0.2114459 | 0.5483137 | 0.9826710 | -0.9090984 | -0.2149840 | -1.1588544 | -0.1766738 | -0.9468539 | 0.0342174 |
| Coprobacter_fastidiosus | -0.0506822 | 0.8212646 | 0.8743250 | 0.3837940 | 0.0885220 | 0.3878452 | 0.3324306 | 0.2957771 | 0.6832163 | 0.4351574 | 0.1711517 | 0.6963755 | 0.1027268 | 0.8189040 | 0.9826710 | -0.0584917 | 0.8260797 | -0.2934091 | 0.9582704 | -0.1899755 | 1.0602903 |
| Coprococcus_catus | -0.9650382 | 0.0000053 | 0.0000339 | 0.0223985 | 0.9130541 | 0.9605496 | -0.0625851 | 0.8293030 | 0.9582446 | 0.1073821 | 0.7111736 | 0.9931883 | 0.1699672 | 0.6787485 | 0.9826710 | -0.3820600 | 0.4268570 | -0.6348990 | 0.5097288 | -0.4642853 | 0.6790495 |
| Coprococcus_comes | -1.2165824 | 0.0000000 | 0.0000004 | -0.5434396 | 0.0104765 | 0.1167873 | -0.8905865 | 0.0031322 | 0.0684256 | -0.1962927 | 0.5090084 | 0.9931883 | 0.6942938 | 0.0999849 | 0.6041638 | -0.9578021 | -0.1290771 | -1.4769146 | -0.3042584 | -0.7819585 | 0.3893731 |
| Coprococcus_eutactus | -0.5007188 | 0.0685548 | 0.1280893 | -0.2139178 | 0.4345741 | 0.7255890 | -0.2427976 | 0.5306755 | 0.8080869 | -0.1850380 | 0.6323053 | 0.9931883 | 0.0577596 | 0.9159087 | 0.9826710 | -0.7531849 | 0.3253493 | -1.0058672 | 0.5202721 | -0.9472457 | 0.5771698 |
| Dorea_formicigenerans | -1.4562886 | 0.0000000 | 0.0000000 | -0.2245237 | 0.2239555 | 0.5213278 | -0.6718095 | 0.0107270 | 0.1409286 | 0.2227621 | 0.3927603 | 0.8782987 | 0.8945716 | 0.0161087 | 0.3267763 | -0.5877197 | 0.1386723 | -1.1857364 | -0.1578826 | -0.2905843 | 0.7361085 |
| Dorea_longicatena | -2.2712591 | 0.0000000 | 0.0000000 | -0.1107162 | 0.5851809 | 0.8025543 | -0.4694052 | 0.1032111 | 0.4022204 | 0.2479727 | 0.3874054 | 0.8782484 | 0.7173779 | 0.0782928 | 0.5878263 | -0.5104639 | 0.2890314 | -1.0350530 | 0.0962427 | -0.3170363 | 0.8129817 |
| Dorea_sp_AF36_15AT | -0.0577438 | 0.8064769 | 0.8708724 | -0.0610864 | 0.7955183 | 0.9001083 | -0.5172080 | 0.1223251 | 0.4342541 | 0.3950352 | 0.2367074 | 0.7493886 | 0.9122432 | 0.0543339 | 0.5300197 | -0.5257945 | 0.4036216 | -1.1747758 | 0.1403597 | -0.2617898 | 1.0518601 |
| Dysosmobacter_SGB15077 | -0.4603851 | 0.0560121 | 0.1104683 | 0.3690354 | 0.1248192 | 0.4487171 | 0.5565276 | 0.1020534 | 0.4022204 | 0.1815431 | 0.5920122 | 0.9931883 | -0.3749844 | 0.4342674 | 0.9815046 | -0.1032994 | 0.8413701 | -0.1118319 | 1.2248871 | -0.4860614 | 0.8491477 |
| Dysosmobacter_welbionis | 1.8572849 | 0.0000000 | 0.0000000 | -0.6159446 | 0.0043220 | 0.0876758 | -0.5988990 | 0.0483940 | 0.2545166 | -0.6329902 | 0.0368773 | 0.4363818 | -0.0340911 | 0.9362563 | 0.9848029 | -1.0361688 | -0.1957204 | -1.1935215 | -0.0042766 | -1.2269410 | -0.0390393 |
| Eggerthella_lenta | -0.7121128 | 0.0046215 | 0.0133930 | -0.0442070 | 0.8587064 | 0.9528434 | 0.2936938 | 0.4037380 | 0.7234323 | -0.3821077 | 0.2771533 | 0.7716817 | -0.6758015 | 0.1748081 | 0.7280069 | -0.5337969 | 0.4453829 | -0.3990821 | 0.9864696 | -1.0741010 | 0.3098856 |
| Enterocloster_citroniae | -0.3924227 | 0.0826290 | 0.1475889 | -0.0327327 | 0.8843597 | 0.9582003 | -0.0517634 | 0.8708761 | 0.9814636 | -0.0137020 | 0.9656404 | 1.0000000 | 0.0380614 | 0.9326087 | 0.9846129 | -0.4764472 | 0.4109819 | -0.6796250 | 0.5760982 | -0.6408544 | 0.6134505 |
| Enterocloster_hominis | -0.5869120 | 0.0005802 | 0.0020597 | -0.4231029 | 0.0123460 | 0.1252238 | -0.6760690 | 0.0048314 | 0.0909210 | -0.1701368 | 0.4726187 | 0.9749986 | 0.5059322 | 0.1322529 | 0.6639826 | -0.7532869 | -0.0929189 | -1.1432835 | -0.2088545 | -0.6368235 | 0.2965500 |
| Escherichia_coli | 0.1013471 | 0.6957599 | 0.8032351 | -0.8303378 | 0.0016028 | 0.0429828 | -0.7921934 | 0.0319261 | 0.2108606 | -0.8684823 | 0.0187127 | 0.2952455 | -0.0762888 | 0.8829654 | 0.9826710 | -1.3412078 | -0.3194679 | -1.5150808 | -0.0693061 | -1.5905531 | -0.1464114 |
| Eubacterium_ramulus | -0.3537106 | 0.0931463 | 0.1613021 | -0.4957961 | 0.0190916 | 0.1643034 | -0.8524856 | 0.0045590 | 0.0909210 | -0.1391066 | 0.6390195 | 0.9931883 | 0.7133790 | 0.0904467 | 0.5878263 | -0.9093452 | -0.0822470 | -1.4376628 | -0.2673085 | -0.7236228 | 0.4454096 |
| Eubacterium_rectale | -0.8886340 | 0.0055440 | 0.0154364 | 0.0102462 | 0.9741811 | 0.9840937 | 0.4783100 | 0.2864924 | 0.6783679 | -0.4578176 | 0.3070255 | 0.8001546 | -0.9361276 | 0.1406125 | 0.6639826 | -0.6139550 | 0.6344474 | -0.4049425 | 1.3615625 | -1.3400724 | 0.4244373 |
| Eubacterium_siraeum | -0.0845427 | 0.7570292 | 0.8431227 | -0.3587257 | 0.1903749 | 0.4996872 | -0.2763885 | 0.4750186 | 0.7797994 | -0.4410628 | 0.2543528 | 0.7568859 | -0.1646743 | 0.7631739 | 0.9826710 | -0.8974267 | 0.1799754 | -1.0386572 | 0.4858802 | -1.2024705 | 0.3203449 |
| Eubacterium_ventriosum | -1.2106706 | 0.0000002 | 0.0000017 | 0.2183481 | 0.3268933 | 0.6631265 | -0.0614242 | 0.8452471 | 0.9616687 | 0.4981205 | 0.1144179 | 0.6732760 | 0.5595446 | 0.2094812 | 0.7678898 | -0.2201206 | 0.6568168 | -0.6818629 | 0.5590145 | -0.1216174 | 1.1178583 |
| Faecalibacterium_SGB15346 | 1.1035100 | 0.0014443 | 0.0047695 | 0.2623097 | 0.4421378 | 0.7300415 | 0.0108100 | 0.9821250 | 0.9973905 | 0.5138093 | 0.2872112 | 0.7788837 | 0.5029992 | 0.4611416 | 0.9815046 | -0.4099823 | 0.9346016 | -0.9404914 | 0.9621115 | -0.4364177 | 1.4640362 |
| Faecalibacterium_prausnitzii | 1.5436646 | 0.0000000 | 0.0000000 | -0.1207767 | 0.5305277 | 0.7830163 | -0.2416882 | 0.3753748 | 0.7060028 | 0.0001347 | 0.9996048 | 1.0000000 | 0.2418229 | 0.5300698 | 0.9826710 | -0.5002199 | 0.2586664 | -0.7786050 | 0.2952287 | -0.5361756 | 0.5364451 |
| Faecalibacterium_sp_CLA_AA_H233 | 0.1236805 | 0.7161661 | 0.8135647 | 0.4635346 | 0.1741299 | 0.4901612 | 0.6135445 | 0.2034695 | 0.5556282 | 0.3135248 | 0.5145312 | 0.9931883 | -0.3000196 | 0.6592521 | 0.9826710 | -0.2070259 | 1.1340952 | -0.3353071 | 1.5623960 | -0.6342550 | 1.2613047 |
| Faecalibacterium_sp_HTFF | 0.5028578 | 0.0964252 | 0.1649684 | 0.4804993 | 0.1120361 | 0.4222573 | 0.4834863 | 0.2575521 | 0.6305585 | 0.4775123 | 0.2629182 | 0.7619261 | -0.0059740 | 0.9920873 | 0.9955929 | -0.1133480 | 1.0743466 | -0.3568151 | 1.3237876 | -0.3618399 | 1.3168645 |
| Faecalicatena_fissicatena | -0.2777654 | 0.2390199 | 0.3554012 | -0.1554422 | 0.5093267 | 0.7827994 | -0.2001755 | 0.5480919 | 0.8080869 | -0.1107089 | 0.7393730 | 0.9931883 | 0.0894666 | 0.8492934 | 0.9826710 | -0.6195741 | 0.3086897 | -0.8569280 | 0.4565770 | -0.7667196 | 0.5453017 |
| Flavonifractor_plautii | 0.8963234 | 0.0008370 | 0.0028298 | -0.4168995 | 0.1153073 | 0.4252894 | -0.0145324 | 0.9689355 | 0.9973905 | -0.8192666 | 0.0291275 | 0.3617661 | -0.8047341 | 0.1284399 | 0.6632169 | -0.9368686 | 0.1030696 | -0.7502952 | 0.7212303 | -1.5541983 | -0.0843349 |
| Fusicatenibacter_saccharivorans | -0.2990210 | 0.1665937 | 0.2643162 | -0.2625046 | 0.2243148 | 0.5213278 | -0.3975887 | 0.1935253 | 0.5389703 | -0.1274205 | 0.6758370 | 0.9931883 | 0.2701682 | 0.5310819 | 0.9826710 | -0.6874706 | 0.1624613 | -0.9989209 | 0.2037434 | -0.7280735 | 0.4732324 |
| Fusicatenibacter_sp_CLA_AA_H277 | 0.2463429 | 0.2083592 | 0.3215979 | -0.1194072 | 0.5412232 | 0.7844941 | -0.2690954 | 0.3309610 | 0.6856880 | 0.0302810 | 0.9126630 | 1.0000000 | 0.2993764 | 0.4438853 | 0.9815046 | -0.5045292 | 0.2657148 | -0.8140478 | 0.2758570 | -0.5140559 | 0.5746179 |
| GGB13404_SGB14252 | 1.1032425 | 0.0000002 | 0.0000018 | 0.0979484 | 0.6302021 | 0.8165266 | 0.1683017 | 0.5588687 | 0.8080869 | 0.0275951 | 0.9235227 | 1.0000000 | -0.1407066 | 0.7294441 | 0.9826710 | -0.3030398 | 0.4989366 | -0.3991016 | 0.7357050 | -0.5391673 | 0.5943575 |
| GGB1420_SGB1957 | 0.3443263 | 0.0243489 | 0.0557669 | -0.1723725 | 0.2568791 | 0.5655322 | -0.1955711 | 0.3629562 | 0.6934416 | -0.1491738 | 0.4870092 | 0.9833147 | 0.0463973 | 0.8784851 | 0.9826710 | -0.4715315 | 0.1267865 | -0.6188848 | 0.2277426 | -0.5720094 | 0.2736617 |
| GGB2653_SGB3574 | -0.5695842 | 0.0044208 | 0.0130783 | 0.5521852 | 0.0057526 | 0.0961022 | 0.6718270 | 0.0172325 | 0.1687600 | 0.4325435 | 0.1228250 | 0.6749058 | -0.2392836 | 0.5450906 | 0.9826710 | 0.1625840 | 0.9417865 | 0.1205364 | 1.2231176 | -0.1181244 | 0.9832113 |
| GGB2998_SGB3988 | 0.7425379 | 0.0001167 | 0.0005714 | -0.0138126 | 0.9415278 | 0.9749077 | 0.3797782 | 0.1553699 | 0.4848906 | -0.4074035 | 0.1272180 | 0.6749058 | -0.7871817 | 0.0378758 | 0.5122248 | -0.3850982 | 0.3574730 | -0.1455955 | 0.9051520 | -0.9321838 | 0.1173768 |
| GGB3034_SGB4030 | -1.0115509 | 0.0000000 | 0.0000000 | 0.4015157 | 0.0136740 | 0.1339112 | 0.0842006 | 0.7122698 | 0.8924991 | 0.7188307 | 0.0018973 | 0.0831380 | 0.6346300 | 0.0505259 | 0.5300197 | 0.0834651 | 0.7195662 | -0.3658449 | 0.5342462 | 0.2692935 | 1.1683678 |
| GGB3109_SGB4121 | -0.8855511 | 0.0000010 | 0.0000073 | -0.1906146 | 0.2741980 | 0.5855055 | -0.6517931 | 0.0088136 | 0.1251536 | 0.2705638 | 0.2721688 | 0.7655571 | 0.9223569 | 0.0087346 | 0.2609051 | -0.5336898 | 0.1524606 | -1.1372488 | -0.1663373 | -0.2143436 | 0.7554712 |
| GGB3175_SGB4191 | 0.6599143 | 0.0131748 | 0.0346450 | -0.2495102 | 0.3446713 | 0.6845220 | -0.0396215 | 0.9154292 | 0.9973905 | -0.4593988 | 0.2187703 | 0.7316337 | -0.4197773 | 0.4264756 | 0.9815046 | -0.7693885 | 0.2703681 | -0.7752558 | 0.6960128 | -1.1942022 | 0.2754045 |
| GGB33469_SGB15236 | 0.6125204 | 0.0443114 | 0.0911916 | -0.2412381 | 0.4258720 | 0.7242374 | -0.3278914 | 0.4443148 | 0.7601531 | -0.1545847 | 0.7178845 | 0.9931883 | 0.1733067 | 0.7746723 | 0.9826710 | -0.8379858 | 0.3555096 | -1.1722969 | 0.5165140 | -0.9980364 | 0.6888669 |
| GGB33512_SGB15203 | 0.4893351 | 0.0056008 | 0.0154429 | -0.1850376 | 0.2899263 | 0.6144707 | 0.2243406 | 0.3643163 | 0.6934416 | -0.5944159 | 0.0169308 | 0.2897371 | -0.8187565 | 0.0200286 | 0.3378885 | -0.5291811 | 0.1591059 | -0.2626267 | 0.7113079 | -1.0808332 | -0.1079986 |
| GGB33586_SGB53517 | 0.4509516 | 0.0200435 | 0.0486526 | -0.3512535 | 0.0691663 | 0.3507721 | -0.0999710 | 0.7133708 | 0.8924991 | -0.6025360 | 0.0277831 | 0.3617661 | -0.5025650 | 0.1924602 | 0.7386309 | -0.7303920 | 0.0278850 | -0.6364568 | 0.4365147 | -1.1384158 | -0.0666563 |
| GGB3537_SGB4727 | -0.0453741 | 0.8183308 | 0.8743250 | 0.4219867 | 0.0338803 | 0.2532106 | 0.3930352 | 0.1609390 | 0.4968117 | 0.4509382 | 0.1076776 | 0.6732760 | 0.0579030 | 0.8834752 | 0.9826710 | 0.0325290 | 0.8114443 | -0.1580523 | 0.9441226 | -0.0995268 | 1.0014031 |
| GGB38744_SGB14842 | -0.5974362 | 0.0055236 | 0.0154364 | 0.8076923 | 0.0002027 | 0.0115115 | 0.7386103 | 0.0150524 | 0.1687600 | 0.8767742 | 0.0039961 | 0.1031732 | 0.1381639 | 0.7454391 | 0.9826710 | 0.3882226 | 1.2271619 | 0.1450555 | 1.3321651 | 0.2838899 | 1.4696586 |
| GGB45432_SGB63101 | -0.0714864 | 0.7617945 | 0.8451158 | 0.4846980 | 0.0411204 | 0.2715858 | 1.1418554 | 0.0007723 | 0.0313313 | -0.1724594 | 0.6049841 | 0.9931883 | -1.3143148 | 0.0058817 | 0.2087999 | 0.0197821 | 0.9496139 | 0.4839936 | 1.7997172 | -0.8295781 | 0.4846594 |
| GGB45613_SGB63326 | -0.3369888 | 0.2098499 | 0.3221480 | 0.4975471 | 0.0648674 | 0.3349516 | 0.6182769 | 0.1045389 | 0.4022204 | 0.3768173 | 0.3207308 | 0.8206087 | -0.2414596 | 0.6525628 | 0.9826710 | -0.0310229 | 1.0261171 | -0.1296562 | 1.3662100 | -0.3702710 | 1.1239056 |
| GGB47687_SGB2286 | 0.6535481 | 0.0054666 | 0.0154364 | -0.0697142 | 0.7642679 | 0.8861676 | 0.0494591 | 0.8804733 | 0.9871353 | -0.1888876 | 0.5655310 | 0.9931883 | -0.2383467 | 0.6083037 | 0.9826710 | -0.5280104 | 0.3885820 | -0.5990357 | 0.6979539 | -0.8366499 | 0.4588748 |
| GGB52106_SGB72838 | -0.3682983 | 0.0279506 | 0.0625036 | 0.2083783 | 0.2113309 | 0.5213278 | 0.2027371 | 0.3895107 | 0.7153866 | 0.2140196 | 0.3631926 | 0.8507175 | 0.0112825 | 0.9729411 | 0.9948202 | -0.1195328 | 0.5362895 | -0.2612613 | 0.6667354 | -0.2494547 | 0.6774938 |
| GGB52130_SGB14966 | 0.4437215 | 0.0187024 | 0.0474239 | -0.1670068 | 0.3726365 | 0.7078181 | -0.2279067 | 0.3898489 | 0.7153866 | -0.1061068 | 0.6883078 | 0.9931883 | 0.1217999 | 0.7448375 | 0.9826710 | -0.5358914 | 0.2018779 | -0.7498831 | 0.2940697 | -0.6274936 | 0.4152800 |
| GGB9062_SGB13981 | -0.0647434 | 0.6986418 | 0.8032966 | 0.2382218 | 0.1554877 | 0.4779906 | 0.0747668 | 0.7520113 | 0.9166147 | 0.4016769 | 0.0905941 | 0.6432181 | 0.3269101 | 0.3289556 | 0.9442582 | -0.0914217 | 0.5678653 | -0.3916829 | 0.5412164 | -0.0642459 | 0.8675997 |
| GGB9063_SGB13982 | 0.2916340 | 0.0454358 | 0.0928328 | 0.0315966 | 0.8273630 | 0.9250831 | -0.0077536 | 0.9698285 | 0.9973905 | 0.0709469 | 0.7290290 | 0.9931883 | 0.0787005 | 0.7859369 | 0.9826710 | -0.2540426 | 0.3172359 | -0.4119367 | 0.3964295 | -0.3327797 | 0.4746735 |
| GGB9064_SGB13983 | 0.8601846 | 0.0000099 | 0.0000613 | 0.0663380 | 0.7253868 | 0.8729231 | 0.4892562 | 0.0684844 | 0.3353373 | -0.3565802 | 0.1827094 | 0.7225423 | -0.8458365 | 0.0262335 | 0.3921212 | -0.3059460 | 0.4386219 | -0.0375302 | 1.0160426 | -0.8827717 | 0.1696112 |
| GGB9342_SGB14306 | 0.5828192 | 0.0260252 | 0.0591292 | 0.2022035 | 0.4368863 | 0.7255890 | -0.1239011 | 0.7361721 | 0.9093663 | 0.5283081 | 0.1515889 | 0.6943751 | 0.6522092 | 0.2105748 | 0.7678898 | -0.3101122 | 0.7145192 | -0.8488343 | 0.6010320 | -0.1958062 | 1.2524224 |
| GGB9345_SGB14311 | 0.5748965 | 0.0274892 | 0.0619598 | -0.0285100 | 0.9122907 | 0.9605496 | -0.0758206 | 0.8360018 | 0.9608298 | 0.0188006 | 0.9590133 | 1.0000000 | 0.0946211 | 0.8549703 | 0.9826710 | -0.5388273 | 0.4818073 | -0.7979259 | 0.6462848 | -0.7024892 | 0.7400903 |
| GGB9453_SGB14844 | -0.1193012 | 0.5063901 | 0.6335453 | 0.0858262 | 0.6325206 | 0.8165266 | 0.3475716 | 0.1722283 | 0.5128561 | -0.1759191 | 0.4881950 | 0.9833147 | -0.5234907 | 0.1459284 | 0.6639826 | -0.2679327 | 0.4395852 | -0.1530017 | 0.8481449 | -0.6759270 | 0.3240888 |
| GGB9502_SGB14899 | 0.2233381 | 0.0723169 | 0.1325734 | -0.1985993 | 0.1096613 | 0.4222573 | -0.3506347 | 0.0464103 | 0.2510951 | -0.0465638 | 0.7899383 | 1.0000000 | 0.3040708 | 0.2199544 | 0.7792030 | -0.4424067 | 0.0452082 | -0.6956253 | -0.0056441 | -0.3911648 | 0.2980371 |
| GGB9509_SGB14906 | 0.3914056 | 0.0206932 | 0.0489740 | -0.2843912 | 0.0914987 | 0.3878452 | 0.0004460 | 0.9985010 | 1.0000000 | -0.5692284 | 0.0173434 | 0.2897371 | -0.5696744 | 0.0909958 | 0.5878263 | -0.6152014 | 0.0464190 | -0.4676545 | 0.4685466 | -1.0368002 | -0.1016565 |
| GGB9522_SGB14921 | 0.3323671 | 0.0911204 | 0.1597419 | 0.2714537 | 0.1670022 | 0.4889550 | 0.3127595 | 0.2600291 | 0.6311817 | 0.2301479 | 0.4062564 | 0.8873087 | -0.0826116 | 0.8329767 | 0.9826710 | -0.1147078 | 0.6576153 | -0.2336638 | 0.8591829 | -0.3156583 | 0.7759541 |
| GGB9531_SGB14932 | 0.0500117 | 0.7529563 | 0.8431227 | 0.0839896 | 0.5971995 | 0.8025543 | 0.1688978 | 0.4528644 | 0.7701406 | -0.0009187 | 0.9967357 | 1.0000000 | -0.1698165 | 0.5931984 | 0.9826710 | -0.2292545 | 0.3972336 | -0.2743465 | 0.6121421 | -0.4436623 | 0.4418250 |
| GGB9534_SGB14937 | 0.8954681 | 0.0001310 | 0.0006199 | -0.0032018 | 0.9888375 | 0.9888375 | 0.0384368 | 0.9055195 | 0.9973905 | -0.0448403 | 0.8897493 | 1.0000000 | -0.0832771 | 0.8556334 | 0.9826710 | -0.4544238 | 0.4480203 | -0.6000481 | 0.6769216 | -0.6826040 | 0.5929233 |
| GGB9602_SGB15031 | 0.5413714 | 0.0404626 | 0.0838788 | -0.6005399 | 0.0232335 | 0.1940679 | -0.8628812 | 0.0212214 | 0.1795889 | -0.3381987 | 0.3626274 | 0.8507175 | 0.5246825 | 0.3183471 | 0.9416957 | -1.1181013 | -0.0829786 | -1.5952369 | -0.1305255 | -1.0697272 | 0.3933298 |
| GGB9614_SGB15049 | 1.9494046 | 0.0000000 | 0.0000000 | 0.3478852 | 0.0767216 | 0.3718112 | 0.5883006 | 0.0347708 | 0.2244297 | 0.1074698 | 0.6975278 | 0.9931883 | -0.4808308 | 0.2200769 | 0.7792030 | -0.0377532 | 0.7335236 | 0.0426174 | 1.1339837 | -0.4375970 | 0.6525366 |
| GGB9619_SGB15067 | 0.6139043 | 0.0005773 | 0.0020597 | 0.1046523 | 0.5502642 | 0.7844941 | 0.1308535 | 0.5975550 | 0.8329130 | 0.0784512 | 0.7512805 | 0.9931883 | -0.0524023 | 0.8810519 | 0.9826710 | -0.2405742 | 0.4498789 | -0.3576464 | 0.6193533 | -0.4094969 | 0.5663992 |
| GGB9621_SGB15073 | 0.6212828 | 0.0001452 | 0.0006651 | -0.1927023 | 0.2291727 | 0.5248794 | -0.1744520 | 0.4410959 | 0.7592196 | -0.2109526 | 0.3512442 | 0.8507175 | -0.0365006 | 0.9091287 | 0.9826710 | -0.5079606 | 0.1225560 | -0.6205465 | 0.2716424 | -0.6565432 | 0.2346380 |
| GGB9635_SGB15106 | -0.0057553 | 0.9873382 | 0.9873382 | -0.4155704 | 0.2527923 | 0.5608830 | -0.7571623 | 0.1414123 | 0.4616646 | -0.0739785 | 0.8852473 | 1.0000000 | 0.6831838 | 0.3468942 | 0.9442582 | -1.1306067 | 0.2994658 | -1.7689476 | 0.2546229 | -1.0846209 | 0.9366639 |
| GGB9646_SGB15123 | 0.4115811 | 0.0664366 | 0.1269839 | 0.1526647 | 0.4940478 | 0.7794976 | 0.1891696 | 0.5491896 | 0.8080869 | 0.1161599 | 0.7126163 | 0.9931883 | -0.0730097 | 0.8700140 | 0.9826710 | -0.2871560 | 0.5924855 | -0.4331823 | 0.8115215 | -0.5054890 | 0.7378088 |
| GGB9667_SGB15164 | 0.9218116 | 0.0000250 | 0.0001339 | 0.0842555 | 0.6921111 | 0.8509071 | 0.3723322 | 0.2171768 | 0.5771735 | -0.2038213 | 0.4981323 | 0.9892978 | -0.5761535 | 0.1768749 | 0.7280069 | -0.3351565 | 0.5036674 | -0.2211410 | 0.9658054 | -0.7966242 | 0.3889815 |
| GGB9699_SGB15216 | 2.0745480 | 0.0000000 | 0.0000000 | -0.1299469 | 0.5355669 | 0.7840258 | -0.2859959 | 0.3356535 | 0.6856880 | 0.0261021 | 0.9298006 | 1.0000000 | 0.3120979 | 0.4570103 | 0.9815046 | -0.5432605 | 0.2833667 | -0.8708397 | 0.2988480 | -0.5580812 | 0.6102853 |
| GGB9708_SGB15234 | 1.4964436 | 0.0000006 | 0.0000047 | -0.2131083 | 0.4595041 | 0.7397360 | -0.2484536 | 0.5421344 | 0.8080869 | -0.1777631 | 0.6622835 | 0.9931883 | 0.0706905 | 0.9022824 | 0.9826710 | -0.7806959 | 0.3544792 | -1.0515971 | 0.5546899 | -0.9799994 | 0.6244732 |
| GGB9715_SGB15265 | -0.2027302 | 0.5574173 | 0.6736447 | -0.1578396 | 0.6477654 | 0.8286728 | -0.2862919 | 0.5582051 | 0.8080869 | -0.0293874 | 0.9519954 | 1.0000000 | 0.2569044 | 0.7100067 | 0.9826710 | -0.8387951 | 0.5231158 | -1.2498523 | 0.6772686 | -0.9918595 | 0.9330847 |
| GGB9719_SGB15272 | 0.1118734 | 0.5213415 | 0.6465545 | 0.1278768 | 0.4636374 | 0.7397360 | 0.2378353 | 0.3356996 | 0.6856880 | 0.0179182 | 0.9420336 | 1.0000000 | -0.2199171 | 0.5284876 | 0.9826710 | -0.2158693 | 0.4716228 | -0.2485697 | 0.7242403 | -0.4679373 | 0.5037738 |
| GGB9719_SGB15273 | -0.1300549 | 0.3512375 | 0.4865924 | 0.1139982 | 0.4137246 | 0.7078181 | 0.4164334 | 0.0359143 | 0.2266593 | -0.1884370 | 0.3393083 | 0.8507175 | -0.6048705 | 0.0311543 | 0.4423904 | -0.1607101 | 0.3887065 | 0.0277178 | 0.8051491 | -0.5767136 | 0.1998396 |
| GGB9730_SGB15291 | 0.9232657 | 0.0000005 | 0.0000041 | -0.2808796 | 0.1121504 | 0.4222573 | -0.5017567 | 0.0454010 | 0.2510951 | -0.0600025 | 0.8095393 | 1.0000000 | 0.4417542 | 0.2108993 | 0.7678898 | -0.6281292 | 0.0663699 | -0.9931192 | -0.0103942 | -0.5508100 | 0.4308049 |
| GGB9758_SGB15368 | 0.0288709 | 0.9459579 | 0.9663743 | 0.1249628 | 0.7692528 | 0.8861676 | -0.0130693 | 0.9826993 | 0.9973905 | 0.2629950 | 0.6623047 | 0.9931883 | 0.2760642 | 0.7459204 | 0.9826710 | -0.7148216 | 0.9647473 | -1.2013748 | 1.1752362 | -0.9239683 | 1.4499582 |
| GGB9760_SGB15373 | 0.7472873 | 0.0000399 | 0.0002058 | -0.1789817 | 0.3131413 | 0.6491396 | -0.2576334 | 0.3048875 | 0.6856880 | -0.1003301 | 0.6887420 | 0.9931883 | 0.1573033 | 0.6571834 | 0.9826710 | -0.5282970 | 0.1703335 | -0.7519188 | 0.2366520 | -0.5940572 | 0.3933971 |
| GGB9765_SGB15382 | -0.0034039 | 0.9861196 | 0.9873382 | 0.3235198 | 0.0996440 | 0.4042698 | 0.4258812 | 0.1253520 | 0.4395057 | 0.2211584 | 0.4243277 | 0.8926598 | -0.2047228 | 0.6010098 | 0.9826710 | -0.0622494 | 0.7092890 | -0.1199871 | 0.9717494 | -0.3240933 | 0.7664101 |
| GGB9770_SGB15390 | 0.0444962 | 0.8158030 | 0.8743250 | -0.0153624 | 0.9358944 | 0.9749077 | 0.2829774 | 0.2959000 | 0.6832163 | -0.3137022 | 0.2462056 | 0.7493886 | -0.5966796 | 0.1196721 | 0.6535935 | -0.3919487 | 0.3612239 | -0.2498969 | 0.8158518 | -0.8459746 | 0.2185702 |
| GGB9775_SGB15395 | 0.4983309 | 0.0001018 | 0.0005074 | -0.3049544 | 0.0158256 | 0.1449832 | -0.0498971 | 0.7783201 | 0.9287518 | -0.5600118 | 0.0018331 | 0.0831380 | -0.5101147 | 0.0430179 | 0.5300197 | -0.5519016 | -0.0580073 | -0.3993304 | 0.2995362 | -0.9090504 | -0.2109732 |
| GGB9781_SGB15402 | -0.5706066 | 0.0060151 | 0.0162694 | 0.4307636 | 0.0371508 | 0.2637708 | 0.5214751 | 0.0740662 | 0.3448326 | 0.3400521 | 0.2422440 | 0.7493886 | -0.1814230 | 0.6586997 | 0.9826710 | 0.0259741 | 0.8355531 | -0.0513071 | 1.0942573 | -0.2320831 | 0.9121873 |
| GGB9818_SGB15459 | 0.8201161 | 0.0000124 | 0.0000735 | 0.0240609 | 0.8949116 | 0.9590750 | 0.4515096 | 0.0812358 | 0.3662056 | -0.4033878 | 0.1185345 | 0.6732760 | -0.8548975 | 0.0199610 | 0.3378885 | -0.3350745 | 0.3831963 | -0.0566715 | 0.9596907 | -0.9109949 | 0.1042193 |
| Gemmiger_formicilis | 0.8442966 | 0.0021758 | 0.0067903 | 0.1020173 | 0.7071175 | 0.8618943 | -0.3691204 | 0.3372615 | 0.6856880 | 0.5731551 | 0.1365649 | 0.6749058 | 0.9422755 | 0.0840648 | 0.5878263 | -0.4332089 | 0.6372435 | -1.1264722 | 0.3882313 | -0.1833412 | 1.3296514 |
| Guopingia_tenuis | -0.1581201 | 0.5011133 | 0.6297176 | 0.8256167 | 0.0005594 | 0.0198577 | 1.5390110 | 0.0000072 | 0.0010247 | 0.1122224 | 0.7353746 | 0.9931883 | -1.4267886 | 0.0027419 | 0.1510606 | 0.3625212 | 1.2887122 | 0.8837251 | 2.1942970 | -0.5423234 | 0.7667682 |
| Holdemania_filiformis | 0.0658600 | 0.7466674 | 0.8431227 | -0.2959396 | 0.1478727 | 0.4772256 | -0.1060722 | 0.7131243 | 0.8924991 | -0.4858070 | 0.0931919 | 0.6455242 | -0.3797348 | 0.3522759 | 0.9442582 | -0.6978547 | 0.1059756 | -0.6747871 | 0.4626428 | -1.0538795 | 0.0822656 |
| Hydrogenoanaerobacterium_saccharovorans | 1.0835949 | 0.0000000 | 0.0000000 | -0.5787780 | 0.0005027 | 0.0198577 | -0.4208769 | 0.0698632 | 0.3362905 | -0.7366790 | 0.0016659 | 0.0831380 | -0.3158021 | 0.3341033 | 0.9442582 | -0.9006389 | -0.2569171 | -0.8763142 | 0.0345603 | -1.1916018 | -0.2817562 |
| Intestinimonas_butyriciproducens | 0.2982007 | 0.2134420 | 0.3241579 | 0.1792461 | 0.4538593 | 0.7397360 | 0.4333247 | 0.2014238 | 0.5553821 | -0.0748325 | 0.8247740 | 1.0000000 | -0.5081572 | 0.2887972 | 0.8633515 | -0.2921948 | 0.6506869 | -0.2337700 | 1.1004193 | -0.7411737 | 0.5915086 |
| Intestinimonas_gabonensis | 0.0179885 | 0.9290781 | 0.9525566 | -0.0589087 | 0.7707161 | 0.8861676 | -0.0953425 | 0.7388845 | 0.9093663 | -0.0224750 | 0.9372893 | 1.0000000 | 0.0728675 | 0.8569462 | 0.9826710 | -0.4573922 | 0.3395748 | -0.6592016 | 0.4685167 | -0.5856972 | 0.5407473 |
| Intestinimonas_massiliensis | 0.1847850 | 0.4059326 | 0.5412435 | 0.4164577 | 0.0621889 | 0.3339497 | 0.6369241 | 0.0440224 | 0.2500470 | 0.1959913 | 0.5326674 | 0.9931883 | -0.4409327 | 0.3216355 | 0.9416957 | -0.0214653 | 0.8543807 | 0.0172575 | 1.2565906 | -0.4229753 | 0.8149579 |
| Lachnoclostridium_sp_An138 | -0.7915945 | 0.0004484 | 0.0017208 | 0.6184502 | 0.0057395 | 0.0961022 | 0.5053205 | 0.1079200 | 0.4086571 | 0.7315799 | 0.0203433 | 0.3040793 | 0.2262594 | 0.6092738 | 0.9826710 | 0.1822150 | 1.0546855 | -0.1119578 | 1.1225989 | 0.1149988 | 1.3481610 |
| Lachnospira_eligens | -1.4168327 | 0.0000006 | 0.0000047 | -0.1412929 | 0.6038984 | 0.8051978 | -0.2333469 | 0.5448986 | 0.8080869 | -0.0492388 | 0.8981769 | 1.0000000 | 0.1841080 | 0.7352974 | 0.9826710 | -0.6780422 | 0.3954565 | -0.9928540 | 0.5261602 | -0.8078880 | 0.7094104 |
| Lachnospira_pectinoschiza | -1.0804390 | 0.0002182 | 0.0009532 | -0.2348543 | 0.4121834 | 0.7078181 | 0.3417383 | 0.3990922 | 0.7225024 | -0.8114469 | 0.0461094 | 0.4850025 | -1.1531851 | 0.0451849 | 0.5300197 | -0.7989291 | 0.3292205 | -0.4564346 | 1.1399111 | -1.6087182 | -0.0141756 |
| Lachnospiraceae_bacterium | 0.2285355 | 0.4203803 | 0.5501751 | 0.7566681 | 0.0082483 | 0.1151234 | 0.3447218 | 0.3904399 | 0.7153866 | 1.1686145 | 0.0039685 | 0.1031732 | 0.8238927 | 0.1472919 | 0.6639826 | 0.1980115 | 1.3153248 | -0.4457844 | 1.1352280 | 0.3790012 | 1.9582277 |
| Lachnospiraceae_bacterium_AM48_27BH | -0.6473736 | 0.0019343 | 0.0061036 | 0.1894153 | 0.3578208 | 0.6964919 | 0.5067397 | 0.0831505 | 0.3689804 | -0.1279090 | 0.6601087 | 0.9931883 | -0.6346488 | 0.1243301 | 0.6538840 | -0.2162028 | 0.5950335 | -0.0672151 | 1.0806945 | -0.7012155 | 0.4453974 |
| Lachnospiraceae_bacterium_CLA_AA_H215 | 0.3468883 | 0.1106220 | 0.1858899 | -0.5685693 | 0.0093790 | 0.1151234 | -0.4650551 | 0.1304917 | 0.4465018 | -0.6720834 | 0.0292980 | 0.3617661 | -0.2070283 | 0.6327976 | 0.9826710 | -0.9955821 | -0.1415565 | -1.0692836 | 0.1391733 | -1.2756294 | -0.0685374 |
| Lachnospiraceae_bacterium_CLA_AA_H244 | 0.6309932 | 0.0045727 | 0.0133880 | -0.3810603 | 0.0843418 | 0.3863401 | -0.4557307 | 0.1440873 | 0.4616646 | -0.3063899 | 0.3246504 | 0.8232206 | 0.1493407 | 0.7340619 | 0.9826710 | -0.8143463 | 0.0522257 | -1.0688358 | 0.1573744 | -0.9188025 | 0.3060226 |
| Lachnotalea_sp_AF33_28 | -0.2781623 | 0.3173061 | 0.4483330 | 0.2851886 | 0.3052744 | 0.6374848 | 0.3315267 | 0.3994116 | 0.7225024 | 0.2388505 | 0.5431107 | 0.9931883 | -0.0926761 | 0.8674969 | 0.9826710 | -0.2624025 | 0.8327797 | -0.4433216 | 1.1063749 | -0.5351225 | 1.0128236 |
| Lacrimispora_amygdalina | 0.2216610 | 0.3244496 | 0.4516848 | 0.2889599 | 0.1994301 | 0.5056979 | 0.5894038 | 0.0650857 | 0.3242866 | -0.0114841 | 0.9711446 | 1.0000000 | -0.6008878 | 0.1822369 | 0.7379384 | -0.1539120 | 0.7318317 | -0.0372655 | 1.2160730 | -0.6374455 | 0.6144773 |
| Lawsonibacter_SGB15145 | 1.3597684 | 0.0000000 | 0.0000000 | -0.1811939 | 0.3596731 | 0.6964919 | -0.2173220 | 0.4373410 | 0.7573466 | -0.1450657 | 0.6035464 | 0.9931883 | 0.0722563 | 0.8549029 | 0.9826710 | -0.5707087 | 0.2083210 | -0.7684904 | 0.3338464 | -0.6956115 | 0.4054801 |
| Lawsonibacter_asaccharolyticus | 1.9588727 | 0.0000000 | 0.0000000 | -0.8992651 | 0.0000500 | 0.0064196 | -0.8427373 | 0.0064474 | 0.1077099 | -0.9557929 | 0.0020492 | 0.0831380 | -0.1130556 | 0.7936870 | 0.9826710 | -1.3253889 | -0.4731413 | -1.4457077 | -0.2397669 | -1.5580823 | -0.3535035 |
| Lawsonibacter_hominis | 0.4849402 | 0.0315789 | 0.0684610 | -0.1495161 | 0.5047078 | 0.7827994 | -0.0105741 | 0.9733839 | 0.9973905 | -0.2884581 | 0.3628030 | 0.8507175 | -0.2778840 | 0.5352710 | 0.9826710 | -0.5911191 | 0.2920868 | -0.6354478 | 0.6142996 | -0.9126260 | 0.3357097 |
| Ligaoa_zhengdingensis | -0.1258158 | 0.6140446 | 0.7295197 | 0.7117978 | 0.0048143 | 0.0911508 | 0.8179839 | 0.0215001 | 0.1795889 | 0.6056117 | 0.0871988 | 0.6432181 | -0.2123722 | 0.6703448 | 0.9826710 | 0.2200954 | 1.2035002 | 0.1222188 | 1.5137490 | -0.0893675 | 1.3005909 |
| Mediterraneibacter_faecis | -1.4536733 | 0.0000000 | 0.0000001 | -0.2829388 | 0.2370095 | 0.5384855 | -1.0963285 | 0.0014031 | 0.0498102 | 0.5304508 | 0.1173646 | 0.6732760 | 1.6267793 | 0.0008143 | 0.0770871 | -0.7536857 | 0.1878081 | -1.7624412 | -0.4302157 | -0.1349096 | 1.1958112 |
| Odoribacter_splanchnicus | 0.2648767 | 0.1859007 | 0.2916895 | -0.1111377 | 0.5780297 | 0.8025543 | -0.3683311 | 0.1935738 | 0.5389703 | 0.1460557 | 0.6049840 | 0.9931883 | 0.5143868 | 0.1989213 | 0.7532486 | -0.5048745 | 0.2825991 | -0.9254736 | 0.1888114 | -0.4104575 | 0.7025689 |
| Oliverpabstia_intestinalis | -0.7052688 | 0.0003081 | 0.0012867 | -0.1007309 | 0.5990899 | 0.8025543 | -0.5984639 | 0.0283904 | 0.1966557 | 0.3970020 | 0.1438264 | 0.6749058 | 0.9954659 | 0.0101055 | 0.2609051 | -0.4783600 | 0.2768981 | -1.1328137 | -0.0641140 | -0.1367443 | 0.9307483 |
| Oscillibacter_sp_ER4 | 0.6283839 | 0.0372485 | 0.0795381 | -0.1308508 | 0.6624328 | 0.8325810 | -0.2234863 | 0.5982897 | 0.8329130 | -0.0382153 | 0.9281038 | 1.0000000 | 0.1852710 | 0.7572418 | 0.9826710 | -0.7216528 | 0.4599512 | -1.0594785 | 0.6125058 | -0.8732632 | 0.7968326 |
| Oscillibacter_sp_MSJ_31 | 0.8697484 | 0.0144744 | 0.0373703 | -0.2125747 | 0.5465890 | 0.7844941 | 0.0310984 | 0.9502725 | 0.9973905 | -0.4562478 | 0.3602904 | 0.8507175 | -0.4873461 | 0.4895938 | 0.9826710 | -0.9073931 | 0.4822437 | -0.9520783 | 1.0142751 | -1.4383139 | 0.5258184 |
| Oscillibacter_sp_PC13 | -0.3972345 | 0.1112721 | 0.1858899 | -0.2096516 | 0.3993022 | 0.7078181 | -0.1168502 | 0.7396606 | 0.9093663 | -0.3024530 | 0.3896454 | 0.8782484 | -0.1856028 | 0.7088344 | 0.9826710 | -0.6995379 | 0.2802348 | -0.8100454 | 0.5763451 | -0.9948652 | 0.3899593 |
| Oscillibacter_valericigenes | 1.4061310 | 0.0000000 | 0.0000005 | -0.2038101 | 0.4062382 | 0.7078181 | -0.0131446 | 0.9697716 | 0.9973905 | -0.3944756 | 0.2558487 | 0.7568859 | -0.3813310 | 0.4371171 | 0.9815046 | -0.6871361 | 0.2795159 | -0.6970570 | 0.6707678 | -1.0776155 | 0.2886643 |
| Oscillospiraceae_bacterium | 1.2006532 | 0.0000111 | 0.0000674 | -0.0414810 | 0.8756886 | 0.9580197 | -0.2455510 | 0.5130897 | 0.8070408 | 0.1625890 | 0.6644973 | 0.9931883 | 0.4081400 | 0.4419333 | 0.9815046 | -0.5642717 | 0.4813096 | -0.9853063 | 0.4942043 | -0.5763308 | 0.9015087 |
| Oscillospiraceae_bacterium_CLA_AA_H250 | 0.8175269 | 0.0001421 | 0.0006618 | -0.2992005 | 0.1557009 | 0.4779906 | -0.4916795 | 0.0995683 | 0.4022204 | -0.1067215 | 0.7193569 | 0.9931883 | 0.3849580 | 0.3602102 | 0.9455563 | -0.7134392 | 0.1150382 | -1.0778324 | 0.0944734 | -0.6922124 | 0.4787693 |
| Oscillospiraceae_bacterium_Marseille_Q3528 | 0.5816455 | 0.0003307 | 0.0013610 | -0.1022951 | 0.5197247 | 0.7830163 | -0.3112280 | 0.1672826 | 0.5054071 | 0.1066378 | 0.6348254 | 0.9931883 | 0.4178658 | 0.1894496 | 0.7379384 | -0.4153930 | 0.2108028 | -0.7542654 | 0.1318094 | -0.3358992 | 0.5491748 |
| Parabacteroides_distasonis | 0.6122706 | 0.0052642 | 0.0151013 | 0.0937553 | 0.6654785 | 0.8325810 | -0.0658529 | 0.8300288 | 0.9582446 | 0.2533635 | 0.4087901 | 0.8873087 | 0.3192164 | 0.4619465 | 0.9815046 | -0.3336671 | 0.5211777 | -0.6706609 | 0.5389552 | -0.3507614 | 0.8574884 |
| Parabacteroides_merdae | 0.1022504 | 0.6455861 | 0.7576299 | 0.0343838 | 0.8770603 | 0.9580197 | 0.0278964 | 0.9293200 | 0.9973905 | 0.0408713 | 0.8964864 | 1.0000000 | 0.0129749 | 0.9767139 | 0.9948202 | -0.4038351 | 0.4726028 | -0.5921889 | 0.6479816 | -0.5785136 | 0.6602562 |
| Paraprevotella_clara | -0.5857004 | 0.1014457 | 0.1720178 | -0.1364271 | 0.7017091 | 0.8589888 | -0.2783744 | 0.5808281 | 0.8281574 | 0.0055202 | 0.9912495 | 1.0000000 | 0.2838946 | 0.6902582 | 0.9826710 | -0.8385634 | 0.5657092 | -1.2719060 | 0.7151572 | -0.9868891 | 0.9979296 |
| Parasutterella_excrementihominis | 0.8118271 | 0.0056638 | 0.0154665 | 0.2259393 | 0.4362976 | 0.7255890 | 0.2803670 | 0.4947214 | 0.7983005 | 0.1715116 | 0.6756781 | 0.9931883 | -0.1088555 | 0.8511171 | 0.9826710 | -0.3457793 | 0.7976578 | -0.5286219 | 1.0893559 | -0.6365635 | 0.9795867 |
| Phascolarctobacterium_faecium | -0.1912047 | 0.4726104 | 0.6025692 | -0.1327721 | 0.6178152 | 0.8158003 | -0.0820245 | 0.8275027 | 0.9582446 | -0.1835197 | 0.6255895 | 0.9931883 | -0.1014952 | 0.8487066 | 0.9826710 | -0.6572385 | 0.3916942 | -0.8241509 | 0.6601019 | -0.9248079 | 0.5577685 |
| Phocaeicola_dorei | -0.4047226 | 0.2898138 | 0.4178027 | -0.9672770 | 0.0120868 | 0.1252238 | -0.3236079 | 0.5492739 | 0.8080869 | -1.6109461 | 0.0032177 | 0.1031732 | -1.2873382 | 0.0931415 | 0.5878263 | -1.7198268 | -0.2147272 | -1.3884753 | 0.7412595 | -2.6746107 | -0.5472815 |
| Phocaeicola_sartorii | -1.8490959 | 0.0000000 | 0.0000000 | 0.2294912 | 0.2491412 | 0.5571346 | 0.0000000 | 1.0000000 | 1.0000000 | 0.4589824 | 0.1036563 | 0.6690543 | 0.4589824 | 0.2491412 | 0.8073470 | -0.1623318 | 0.6213142 | -0.5544344 | 0.5544344 | -0.0948258 | 1.0127905 |
| Phocaeicola_vulgatus | -0.6355390 | 0.0723552 | 0.1325734 | 0.4617757 | 0.1906478 | 0.4996872 | 0.3701501 | 0.4576813 | 0.7709511 | 0.5534014 | 0.2668141 | 0.7654060 | 0.1832513 | 0.7946109 | 0.9826710 | -0.2321056 | 1.1556570 | -0.6117006 | 1.3520008 | -0.4273403 | 1.5341431 |
| Phocea_massiliensis | -0.0100617 | 0.9577975 | 0.9714803 | 0.0579048 | 0.7607483 | 0.8861676 | 0.1794723 | 0.5050217 | 0.8057649 | -0.0636628 | 0.8127571 | 1.0000000 | -0.2431350 | 0.5228466 | 0.9826710 | -0.3169831 | 0.4327926 | -0.3509987 | 0.7099433 | -0.5935346 | 0.4662091 |
| Provencibacterium_massiliense | -0.2413713 | 0.2941269 | 0.4218789 | 0.6898911 | 0.0030466 | 0.0665572 | 1.0148027 | 0.0020921 | 0.0639477 | 0.3649796 | 0.2618234 | 0.7619261 | -0.6498231 | 0.1584590 | 0.6815147 | 0.2370368 | 1.1427455 | 0.3740081 | 1.6555972 | -0.2750912 | 1.0050503 |
| Pseudoflavonifractor_capillosus | 0.1817008 | 0.4378126 | 0.5677569 | 0.2876177 | 0.2200256 | 0.5213278 | 0.3629458 | 0.2738353 | 0.6590613 | 0.2122897 | 0.5211640 | 0.9931883 | -0.1506561 | 0.7475198 | 0.9826710 | -0.1736841 | 0.7489196 | -0.2898021 | 1.0156937 | -0.4397209 | 0.8643003 |
| Roseburia_faecis | -0.3893694 | 0.1767272 | 0.2788362 | -0.1889794 | 0.5111342 | 0.7827994 | -0.3272513 | 0.4214828 | 0.7400735 | -0.0507076 | 0.9006665 | 1.0000000 | 0.2765437 | 0.6305777 | 0.9826710 | -0.7556691 | 0.3777103 | -1.1291243 | 0.4746218 | -0.8516749 | 0.7502597 |
| Roseburia_hominis | -0.2859875 | 0.2694934 | 0.3924929 | 0.8663516 | 0.0009833 | 0.0310291 | 0.5702630 | 0.1203781 | 0.4327516 | 1.1624402 | 0.0017285 | 0.0831380 | 0.5921773 | 0.2530066 | 0.8073470 | 0.3566663 | 1.3760369 | -0.1509481 | 1.2914740 | 0.4420438 | 1.8828367 |
| Roseburia_intestinalis | -0.5229867 | 0.0741642 | 0.1350169 | 0.0327740 | 0.9104664 | 0.9605496 | 0.0164864 | 0.9681119 | 0.9973905 | 0.0490616 | 0.9051982 | 1.0000000 | 0.0325753 | 0.9554335 | 0.9948202 | -0.5418651 | 0.6074132 | -0.7966352 | 0.8296080 | -0.7631415 | 0.8612648 |
| Roseburia_inulinivorans | -1.0431121 | 0.0002938 | 0.0012456 | -0.3791003 | 0.1804782 | 0.4976292 | -0.2064062 | 0.6054739 | 0.8388028 | -0.5517944 | 0.1679050 | 0.6963755 | -0.3453882 | 0.5409108 | 0.9826710 | -0.9356571 | 0.1774564 | -0.9939410 | 0.5811286 | -1.3384396 | 0.2348508 |
| Ruminococcus_bicirculans | -0.1047783 | 0.6955478 | 0.8032351 | -0.4393053 | 0.1021796 | 0.4087186 | -0.8579763 | 0.0246095 | 0.1839238 | -0.0206343 | 0.9565062 | 1.0000000 | 0.8373420 | 0.1191864 | 0.6535935 | -0.9670832 | 0.0884726 | -1.6047886 | -0.1111640 | -0.7666031 | 0.7253344 |
| Ruminococcus_bromii | -1.3652069 | 0.0000019 | 0.0000133 | -0.3373149 | 0.2233416 | 0.5213278 | -0.5313707 | 0.1754555 | 0.5128561 | -0.1432592 | 0.7138742 | 0.9931883 | 0.3881115 | 0.4829241 | 0.9826710 | -0.8822390 | 0.2076091 | -1.3024450 | 0.2397036 | -0.9134625 | 0.6269442 |
| Ruminococcus_torques | -1.1589855 | 0.0000001 | 0.0000010 | 0.1739815 | 0.4039641 | 0.7078181 | -0.8929241 | 0.0028037 | 0.0663551 | 1.2408871 | 0.0000402 | 0.0114147 | 2.1338112 | 0.0000008 | 0.0002314 | -0.2366105 | 0.5845735 | -1.4739169 | -0.3119313 | 0.6605506 | 1.8212237 |
| Ruthenibacterium_lactatiformans | 0.8552637 | 0.0000421 | 0.0002135 | -0.6232332 | 0.0025233 | 0.0597181 | -0.8921945 | 0.0022517 | 0.0639477 | -0.3542718 | 0.2189749 | 0.7316337 | 0.5379228 | 0.1873031 | 0.7379384 | -1.0243234 | -0.2221429 | -1.4597422 | -0.3246468 | -0.9211784 | 0.2126349 |
| Segatella_copri | -0.1041270 | 0.8348932 | 0.8749434 | 1.0330103 | 0.0399354 | 0.2700392 | 0.1368109 | 0.8465393 | 0.9616687 | 1.9292096 | 0.0069016 | 0.1507742 | 1.7923987 | 0.0742296 | 0.5855892 | 0.0480735 | 2.0179470 | -1.2568869 | 1.5305087 | 0.5370861 | 3.3213332 |
| Simiaoa_sunii | -0.2363296 | 0.5239407 | 0.6469529 | -0.3579564 | 0.3348070 | 0.6696140 | -0.6887912 | 0.1902072 | 0.5389703 | -0.0271216 | 0.9587069 | 1.0000000 | 0.6616696 | 0.3726144 | 0.9620225 | -1.0886706 | 0.3727577 | -1.7227608 | 0.3451784 | -1.0599233 | 1.0056801 |
| Streptococcus_salivarius | -0.4179784 | 0.0877112 | 0.1547204 | -0.0171126 | 0.9440127 | 0.9749077 | 0.0061247 | 0.9858280 | 0.9973905 | -0.0403498 | 0.9067381 | 1.0000000 | -0.0464745 | 0.9240278 | 0.9826710 | -0.4975543 | 0.4633291 | -0.6737064 | 0.6859557 | -0.7194130 | 0.6387133 |
| Streptococcus_thermophilus | -0.6572501 | 0.0003886 | 0.0015543 | -0.0137621 | 0.9396140 | 0.9749077 | -0.3507073 | 0.1736996 | 0.5128561 | 0.3231831 | 0.2092628 | 0.7316337 | 0.6738903 | 0.0650362 | 0.5597053 | -0.3719441 | 0.3444199 | -0.8575392 | 0.1561247 | -0.1830764 | 0.8294426 |
| Sutterella_wadsworthensis | 1.4557556 | 0.0001249 | 0.0006012 | 0.5439886 | 0.1437487 | 0.4692485 | 0.2625218 | 0.6170311 | 0.8465547 | 0.8254554 | 0.1167046 | 0.6732760 | 0.5629336 | 0.4482851 | 0.9815046 | -0.1872299 | 1.2752071 | -0.7721615 | 1.2972051 | -0.2080592 | 1.8589700 |
| Vescimonas_coprocola | 1.3129706 | 0.0000000 | 0.0000002 | -0.3893766 | 0.0785517 | 0.3718112 | -0.6790551 | 0.0305588 | 0.2066360 | -0.0996981 | 0.7488483 | 0.9931883 | 0.5793570 | 0.1896814 | 0.7379384 | -0.8237049 | 0.0449517 | -1.2936350 | -0.0644751 | -0.7135839 | 0.5141877 |
| Wansuia_hejianensis | -1.1041237 | 0.0004405 | 0.0017135 | 0.1375377 | 0.6554774 | 0.8325810 | 0.4232449 | 0.3324511 | 0.6856880 | -0.1481694 | 0.7337735 | 0.9931883 | -0.5714143 | 0.3545101 | 0.9442582 | -0.4700739 | 0.7451494 | -0.4365332 | 1.2830230 | -1.0069764 | 0.7106375 |
| Youxingia_wuxianensis | -0.4377250 | 0.1017570 | 0.1720178 | 0.6868936 | 0.0106918 | 0.1167873 | 1.1477132 | 0.0026781 | 0.0663551 | 0.2260740 | 0.5484359 | 0.9931883 | -0.9216392 | 0.0850760 | 0.5878263 | 0.1616680 | 1.2121191 | 0.4045125 | 1.8909139 | -0.5162872 | 0.9684352 |
| bacterium_210917_DFI_7_65 | 0.3618194 | 0.0314552 | 0.0684610 | -0.2681676 | 0.1096934 | 0.4222573 | -0.1721624 | 0.4666036 | 0.7735065 | -0.3641727 | 0.1242124 | 0.6749058 | -0.1920103 | 0.5655384 | 0.9826710 | -0.5974095 | 0.0610743 | -0.6380438 | 0.2937190 | -0.8295279 | 0.1011825 |
| Bacteroides_faecis | 0.0789161 | 0.7127340 | 0.8129174 | -0.0093742 | 0.9651077 | 0.9832997 | 0.1221415 | 0.6871648 | 0.8835689 | -0.1408899 | 0.6419269 | 0.9931883 | -0.2630314 | 0.5396354 | 0.9826710 | -0.4318877 | 0.4131393 | -0.4757204 | 0.7200034 | -0.7380765 | 0.4562967 |
| Clostridiaceae_unclassified_SGB4771 | 0.4615174 | 0.0136171 | 0.0354795 | 0.1625183 | 0.3810267 | 0.7078181 | 0.2687619 | 0.3061427 | 0.6856880 | 0.0562748 | 0.8298847 | 1.0000000 | -0.2124871 | 0.5666020 | 0.9826710 | -0.2028356 | 0.5278722 | -0.2482185 | 0.7857422 | -0.4601216 | 0.5726712 |
| Clostridium_sp_AM49_4BH | -0.4396135 | 0.0383255 | 0.0810006 | 0.0726905 | 0.7303024 | 0.8751303 | 0.1737274 | 0.5605392 | 0.8080869 | -0.0283465 | 0.9242152 | 1.0000000 | -0.2020739 | 0.6318888 | 0.9826710 | -0.3429916 | 0.4883725 | -0.4144679 | 0.7619227 | -0.6158774 | 0.5591845 |
| Colidextribacter_sp_210702_DFI_3_9 | 0.1991055 | 0.2176704 | 0.3270814 | -0.0957784 | 0.5524607 | 0.7844941 | -0.0560480 | 0.8058414 | 0.9471457 | -0.1355087 | 0.5520673 | 0.9931883 | -0.0794606 | 0.8052615 | 0.9826710 | -0.4134818 | 0.2219251 | -0.5056024 | 0.3935063 | -0.5845552 | 0.3135379 |
| Enterocloster_lavalensis | -0.4474452 | 0.0870625 | 0.1545359 | -0.3699728 | 0.1565251 | 0.4779906 | -0.2230924 | 0.5449670 | 0.8080869 | -0.5168533 | 0.1613622 | 0.6963755 | -0.2937608 | 0.5727743 | 0.9826710 | -0.8832221 | 0.1432764 | -0.9493465 | 0.5031616 | -1.2422870 | 0.2085805 |
| GGB2982_SGB3964 | -0.8860770 | 0.0000000 | 0.0000004 | -0.2014363 | 0.1913554 | 0.4996872 | -0.2550869 | 0.2420356 | 0.6192621 | -0.1477856 | 0.4968118 | 0.9892978 | 0.1073012 | 0.7272015 | 0.9826710 | -0.5046075 | 0.1017350 | -0.6840779 | 0.1739042 | -0.5762921 | 0.2807209 |
| GGB3304_SGB4367 | -0.0673165 | 0.8493379 | 0.8868087 | 0.0101433 | 0.9771634 | 0.9840937 | -0.4883264 | 0.3308050 | 0.6856880 | 0.5086129 | 0.3106256 | 0.8019788 | 0.9969393 | 0.1607799 | 0.6815147 | -0.6885100 | 0.7087965 | -1.4769295 | 0.5002767 | -0.4788736 | 1.4960994 |
| GGB3619_SGB4894 | -0.2683504 | 0.1467404 | 0.2371081 | -0.0177214 | 0.9234074 | 0.9677037 | 0.0249808 | 0.9236973 | 0.9973905 | -0.0604235 | 0.8166058 | 1.0000000 | -0.0854043 | 0.8168076 | 0.9826710 | -0.3811426 | 0.3456998 | -0.4892647 | 0.5392263 | -0.5740882 | 0.4532411 |
| GGB9296_SGB14253 | 0.3806099 | 0.0155446 | 0.0397718 | 0.1003910 | 0.5198547 | 0.7830163 | -0.2000293 | 0.3651202 | 0.6934416 | 0.4008112 | 0.0703175 | 0.6187951 | 0.6008406 | 0.0553420 | 0.5300197 | -0.2069746 | 0.4077565 | -0.6349555 | 0.2348968 | -0.0336236 | 0.8352461 |
| GGB9524_SGB14924 | -0.0119401 | 0.9499163 | 0.9669399 | -0.2520040 | 0.1861311 | 0.4996872 | -0.0207228 | 0.9385911 | 0.9973905 | -0.4832852 | 0.0734797 | 0.6187951 | -0.4625624 | 0.2247831 | 0.7792030 | -0.6268029 | 0.1227949 | -0.5510679 | 0.5096223 | -1.0130313 | 0.0464609 |
| GGB9574_SGB14987 | -0.4419731 | 0.0394968 | 0.0824787 | -0.3269348 | 0.1266194 | 0.4494990 | -0.1542460 | 0.6093783 | 0.8401138 | -0.4996236 | 0.0988141 | 0.6526324 | -0.3453776 | 0.4185308 | 0.9815046 | -0.7473949 | 0.0935253 | -0.7492022 | 0.4407102 | -1.0939078 | 0.0946606 |
| GGB9619_SGB15066 | -0.4246423 | 0.0239306 | 0.0552544 | -0.3185963 | 0.0891093 | 0.3878452 | 0.1406080 | 0.5944457 | 0.8329130 | -0.7778005 | 0.0036012 | 0.1031732 | -0.9184085 | 0.0147353 | 0.3219095 | -0.6864301 | 0.0492376 | -0.3798815 | 0.6610975 | -1.2977021 | -0.2578989 |
| GGB9707_SGB15229 | 0.7627442 | 0.0000137 | 0.0000793 | 0.3176839 | 0.0634975 | 0.3339497 | 0.2351989 | 0.3297158 | 0.6856880 | 0.4001689 | 0.0978007 | 0.6526324 | 0.1649700 | 0.6282270 | 0.9826710 | -0.0180582 | 0.6534260 | -0.2398803 | 0.7102781 | -0.0743737 | 0.8747115 |
| GGB9708_SGB15233 | -0.0800176 | 0.7569525 | 0.8431227 | 0.6390531 | 0.0143199 | 0.1355621 | 0.3570830 | 0.3296891 | 0.6856880 | 0.9210233 | 0.0125451 | 0.2375212 | 0.5639404 | 0.2762677 | 0.8436038 | 0.1293520 | 1.1487543 | -0.3641505 | 1.0783164 | 0.2006045 | 1.6414421 |
| GGB9760_SGB15374 | -0.0583757 | 0.7862139 | 0.8587875 | -0.5798821 | 0.0076977 | 0.1151234 | -0.6279265 | 0.0404917 | 0.2446731 | -0.5318378 | 0.0818042 | 0.6333906 | 0.0960888 | 0.8233516 | 0.9826710 | -1.0041877 | -0.1555766 | -1.2283242 | -0.0275288 | -1.1315573 | 0.0678818 |
| Roseburia_sp_AF02_12 | -0.0265258 | 0.9187149 | 0.9453443 | 0.3951687 | 0.1297825 | 0.4550398 | 0.8700957 | 0.0189943 | 0.1795889 | -0.0797583 | 0.8281391 | 1.0000000 | -0.9498541 | 0.0690824 | 0.5770416 | -0.1173052 | 0.9076426 | 0.1449388 | 1.5952527 | -0.8040962 | 0.6445795 |
| Segatella_brunsvicensis | -0.1893936 | 0.5455330 | 0.6649415 | -0.6067839 | 0.0540313 | 0.3264869 | -0.3215060 | 0.4684617 | 0.7735065 | -0.8920618 | 0.0451791 | 0.4850025 | -0.5705558 | 0.3629072 | 0.9455563 | -1.2242047 | 0.0106370 | -1.1951642 | 0.5521523 | -1.7647332 | -0.0193904 |
| Wujia_chipingensis | -0.3541156 | 0.2528818 | 0.3737999 | -0.3409640 | 0.2708639 | 0.5827678 | -0.5048523 | 0.2493397 | 0.6211620 | -0.1770757 | 0.6853076 | 0.9931883 | 0.3277766 | 0.5961061 | 0.9826710 | -0.9503757 | 0.2684477 | -1.3671774 | 0.3574728 | -1.0384268 | 0.6842754 |
| Alistipes_dispar | 0.4417497 | 0.0115357 | 0.0306181 | 0.0463551 | 0.7889463 | 0.8998423 | 0.0694649 | 0.7768118 | 0.9287518 | 0.0232453 | 0.9243321 | 1.0000000 | -0.0462197 | 0.8938298 | 0.9826710 | -0.2950493 | 0.3877594 | -0.4136265 | 0.5525564 | -0.4593005 | 0.5057910 |
| Alistipes_sp_AF17_16 | 0.3054584 | 0.0666218 | 0.1269839 | -0.0681526 | 0.6808713 | 0.8425971 | -0.5632969 | 0.0172252 | 0.1687600 | 0.4269917 | 0.0696389 | 0.6187951 | 0.9902886 | 0.0031914 | 0.1510606 | -0.3947940 | 0.2584888 | -1.0254986 | -0.1010952 | -0.0346879 | 0.8886713 |
| Anaerobutyricum_soehngenii | 0.3472927 | 0.1237902 | 0.2055930 | 0.3300713 | 0.1433974 | 0.4692485 | 0.6018775 | 0.0598961 | 0.3092817 | 0.0582650 | 0.8545275 | 1.0000000 | -0.5436125 | 0.2277248 | 0.7792030 | -0.1132123 | 0.7733548 | -0.0253742 | 1.2291293 | -0.5682782 | 0.6848082 |
| Anaerosacchariphilus_sp_NSJ_68 | 0.4661447 | 0.0824459 | 0.1475889 | -0.0816167 | 0.7600224 | 0.8861676 | 0.2315507 | 0.5404370 | 0.8080869 | -0.3947841 | 0.2966156 | 0.7947059 | -0.6263348 | 0.2421135 | 0.7995375 | -0.6083719 | 0.4451384 | -0.5138145 | 0.9769158 | -1.1393073 | 0.3497391 |
| Anaerotignum_sp_MSJ_24 | 0.1388950 | 0.4129350 | 0.5429330 | -0.1980172 | 0.2436144 | 0.5490991 | -0.2746018 | 0.2531165 | 0.6250878 | -0.1214325 | 0.6123227 | 0.9931883 | 0.1531693 | 0.6514369 | 0.9826710 | -0.5321541 | 0.1361197 | -0.7474097 | 0.1982061 | -0.5937064 | 0.3508413 |
| Bittarella_massiliensis | -0.7916882 | 0.0001665 | 0.0007505 | 0.1749451 | 0.3955252 | 0.7078181 | 0.5910586 | 0.0435791 | 0.2500470 | -0.2411683 | 0.4072631 | 0.8873087 | -0.8322270 | 0.0443762 | 0.5300197 | -0.2305783 | 0.5804686 | 0.0172378 | 1.1648794 | -0.8143410 | 0.3320043 |
| Blautia_SGB4815 | -0.0629407 | 0.7987501 | 0.8658207 | -0.3001179 | 0.2250930 | 0.5213278 | -0.3355400 | 0.3374033 | 0.6856880 | -0.2646958 | 0.4484352 | 0.9364381 | 0.0708442 | 0.8858949 | 0.9826710 | -0.7867956 | 0.1865598 | -1.0241950 | 0.3531150 | -0.9525730 | 0.4231814 |
| Blautia_luti | 0.0349915 | 0.8842407 | 0.9198694 | -0.3145323 | 0.1917813 | 0.4996872 | -0.1555712 | 0.6474347 | 0.8673181 | -0.4734933 | 0.1645963 | 0.6963755 | -0.3179221 | 0.5086164 | 0.9826710 | -0.7883750 | 0.1593105 | -0.8260646 | 0.5149221 | -1.1432293 | 0.1962427 |
| Blautia_sp_OF03_15BH | 0.1564994 | 0.4731441 | 0.6025692 | 0.1366827 | 0.5308861 | 0.7830163 | -0.0129322 | 0.9665572 | 0.9973905 | 0.2862976 | 0.3534081 | 0.8507175 | 0.2992299 | 0.4928000 | 0.9826710 | -0.2931073 | 0.5664727 | -0.6210904 | 0.5952259 | -0.3211736 | 0.8937689 |
| Butyricimonas_paravirosa | 0.2950980 | 0.0801592 | 0.1450013 | 0.3161937 | 0.0609933 | 0.3339497 | 0.1609817 | 0.4982153 | 0.7993964 | 0.4714057 | 0.0482653 | 0.4895481 | 0.3104240 | 0.3557593 | 0.9442582 | -0.0147552 | 0.6471425 | -0.3073151 | 0.6292784 | 0.0036379 | 0.9391734 |
| Catenibacillus_scindens | -0.5340728 | 0.0198504 | 0.0486526 | 0.1458395 | 0.5215268 | 0.7830163 | 0.1835638 | 0.5685102 | 0.8154389 | 0.1081152 | 0.7366043 | 0.9931883 | -0.0754486 | 0.8682323 | 0.9826710 | -0.3024717 | 0.5941506 | -0.4508021 | 0.8179296 | -0.5255341 | 0.7417644 |
| Clostridiaceae_bacterium_Marseille_Q4149 | 0.1807571 | 0.4714150 | 0.6025692 | -0.6713435 | 0.0080981 | 0.1151234 | -0.5308988 | 0.1359868 | 0.4597647 | -0.8117882 | 0.0230925 | 0.3279139 | -0.2808894 | 0.5756552 | 0.9826710 | -1.1658147 | -0.1768723 | -1.2305817 | 0.1687841 | -1.5106807 | -0.1128956 |
| Clostridium_SGB6173 | 0.0403818 | 0.8284416 | 0.8746372 | 0.2556415 | 0.1713190 | 0.4901612 | 0.6779040 | 0.0109170 | 0.1409286 | -0.1666210 | 0.5272146 | 0.9931883 | -0.8445250 | 0.0245475 | 0.3873056 | -0.1117491 | 0.6230320 | 0.1580418 | 1.1977662 | -0.6858960 | 0.3526540 |
| Clostridium_SGB6179 | 0.1688982 | 0.3854633 | 0.5237874 | 0.1073700 | 0.5808815 | 0.8025543 | 0.4356940 | 0.1145848 | 0.4279945 | -0.2209541 | 0.4217385 | 0.8926598 | -0.6566480 | 0.0926353 | 0.5878263 | -0.2758927 | 0.4906326 | -0.1066275 | 0.9780154 | -0.7626629 | 0.3207548 |
| Clostridium_sp_Marseille_P3244 | 0.2250229 | 0.3807563 | 0.5198789 | 0.3844349 | 0.1351631 | 0.4665397 | 0.5700606 | 0.1175478 | 0.4279945 | 0.1988093 | 0.5834944 | 0.9931883 | -0.3712513 | 0.4694842 | 0.9826710 | -0.1211465 | 0.8900164 | -0.1453434 | 1.2854646 | -0.5157866 | 0.9134053 |
| Clostridium_sp_NSJ_42 | 0.2600848 | 0.1469402 | 0.2371081 | 0.2764447 | 0.1233140 | 0.4487171 | 0.6316061 | 0.0133702 | 0.1650927 | -0.0787167 | 0.7553827 | 0.9931883 | -0.7103228 | 0.0482540 | 0.5300197 | -0.0759580 | 0.6288473 | 0.1329519 | 1.1302602 | -0.5768076 | 0.4193742 |
| Coprobacter_secundus | -0.3775626 | 0.0533082 | 0.1058709 | 0.0948710 | 0.6254073 | 0.8165266 | 0.1618368 | 0.5562300 | 0.8080869 | 0.0279052 | 0.9190482 | 1.0000000 | -0.1339317 | 0.7303452 | 0.9826710 | -0.2881379 | 0.4778799 | -0.3801256 | 0.7037992 | -0.5134450 | 0.5692554 |
| Eubacteriaceae_bacterium | -0.5982870 | 0.0325065 | 0.0699382 | 0.0627743 | 0.8212655 | 0.9218949 | 0.1499005 | 0.7030581 | 0.8924991 | -0.0243520 | 0.9505545 | 1.0000000 | -0.1742524 | 0.7538745 | 0.9826710 | -0.4850378 | 0.6105864 | -0.6252605 | 0.9250614 | -0.7986374 | 0.7499334 |
| Faecalibacillus_faecis | -0.0435143 | 0.8219887 | 0.8743250 | -0.0886230 | 0.6468761 | 0.8286728 | -0.0617467 | 0.8214959 | 0.9582446 | -0.1154992 | 0.6727141 | 0.9931883 | -0.0537525 | 0.8894749 | 0.9826710 | -0.4699289 | 0.2926829 | -0.6012993 | 0.4778059 | -0.6544424 | 0.4234439 |
| Faecalibacillus_intestinalis | -1.7170453 | 0.0000000 | 0.0000000 | -0.3112619 | 0.1632817 | 0.4843937 | -0.7352125 | 0.0206211 | 0.1795889 | 0.1126886 | 0.7202678 | 0.9931883 | 0.8479011 | 0.0582242 | 0.5334086 | -0.7501495 | 0.1276257 | -1.3562439 | -0.1141810 | -0.5076414 | 0.7330186 |
| GGB13489_SGB15224 | 0.6984899 | 0.0000061 | 0.0000388 | -0.0945234 | 0.5278201 | 0.7830163 | -0.2061910 | 0.3308308 | 0.6856880 | 0.0171442 | 0.9353903 | 1.0000000 | 0.2233353 | 0.4558702 | 0.9815046 | -0.3895387 | 0.2004919 | -0.6236414 | 0.2112593 | -0.3998346 | 0.4341230 |
| GGB2970_SGB3952 | -0.4794550 | 0.0000320 | 0.0001682 | -0.2280363 | 0.0434524 | 0.2804653 | -0.2305924 | 0.1477506 | 0.4662351 | -0.2254802 | 0.1564177 | 0.6950289 | 0.0051121 | 0.9818270 | 0.9948202 | -0.4492868 | -0.0067858 | -0.5436646 | 0.0824798 | -0.5381988 | 0.0872384 |
| GGB3352_SGB4436 | 0.0422840 | 0.8320377 | 0.8749434 | 0.0288764 | 0.8848337 | 0.9582003 | -0.0280124 | 0.9208988 | 0.9973905 | 0.0857653 | 0.7608724 | 0.9943154 | 0.1137778 | 0.7753925 | 0.9826710 | -0.3641865 | 0.4219394 | -0.5842014 | 0.5281765 | -0.4697954 | 0.6413260 |
| GGB34797_SGB14322 | -0.2328707 | 0.0946398 | 0.1628951 | -0.1937687 | 0.1637387 | 0.4843937 | -0.3925484 | 0.0468593 | 0.2510951 | 0.0050110 | 0.9796111 | 1.0000000 | 0.3975594 | 0.1531777 | 0.6692687 | -0.4672862 | 0.0797488 | -0.7795791 | -0.0055177 | -0.3815826 | 0.3916045 |
| GGB34900_SGB14891 | -0.4017370 | 0.0714289 | 0.1325734 | 0.3865246 | 0.0827192 | 0.3851189 | 0.4782671 | 0.1287807 | 0.4460210 | 0.2947822 | 0.3475620 | 0.8507175 | -0.1834849 | 0.6791296 | 0.9826710 | -0.0506505 | 0.8236998 | -0.1403412 | 1.0968754 | -0.3231274 | 0.9126917 |
| GGB3653_SGB4964 | -0.6468103 | 0.0016089 | 0.0051571 | -0.1207795 | 0.5499355 | 0.7844941 | -0.0096144 | 0.9731551 | 0.9973905 | -0.2319446 | 0.4168347 | 0.8926598 | -0.2223302 | 0.5821052 | 0.9826710 | -0.5188776 | 0.2773186 | -0.5729282 | 0.5536994 | -0.7946221 | 0.3307330 |
| GGB4456_SGB6141 | 0.8210081 | 0.0000018 | 0.0000133 | 0.2439652 | 0.1431954 | 0.4692485 | 0.5715070 | 0.0159565 | 0.1687600 | -0.0835766 | 0.7218815 | 0.9931883 | -0.6550835 | 0.0499554 | 0.5300197 | -0.0835120 | 0.5714424 | 0.1081227 | 1.0348912 | -0.5464375 | 0.3792843 |
| GGB4552_SGB6276 | -1.0711535 | 0.0000014 | 0.0000103 | -0.3602986 | 0.0934772 | 0.3904046 | -0.1280490 | 0.6722914 | 0.8835689 | -0.5925482 | 0.0513297 | 0.5026774 | -0.4644993 | 0.2783803 | 0.8436038 | -0.7819797 | 0.0613825 | -0.7247330 | 0.4686351 | -1.1885584 | 0.0034619 |
| GGB51441_SGB71759 | 0.4990769 | 0.0189686 | 0.0476732 | -0.0639488 | 0.7617701 | 0.8861676 | -0.0868041 | 0.7711910 | 0.9280434 | -0.0410935 | 0.8903636 | 1.0000000 | 0.0457106 | 0.9137087 | 0.9826710 | -0.4797994 | 0.3519018 | -0.6752379 | 0.5016297 | -0.6288626 | 0.5466756 |
| GGB58158_SGB79798 | -0.5324471 | 0.0661131 | 0.1269839 | 0.5180488 | 0.0737022 | 0.3672179 | 0.9886311 | 0.0162879 | 0.1687600 | 0.0474664 | 0.9072472 | 1.0000000 | -0.9411647 | 0.1039520 | 0.6150495 | -0.0502459 | 1.0863434 | 0.1844871 | 1.7927752 | -0.7557693 | 0.8507022 |
| GGB9365_SGB14341 | 0.1584319 | 0.3889591 | 0.5260209 | 0.1681830 | 0.3605081 | 0.6964919 | 0.0126137 | 0.9612953 | 0.9973905 | 0.3237524 | 0.2135024 | 0.7316337 | 0.3111387 | 0.3975663 | 0.9815046 | -0.1939929 | 0.5303589 | -0.4998697 | 0.5250970 | -0.1881522 | 0.8356569 |
| GGB9412_SGB14770 | -0.0512085 | 0.7716316 | 0.8526980 | 0.2391891 | 0.1763663 | 0.4910590 | 0.1737368 | 0.4867589 | 0.7899402 | 0.3046414 | 0.2228544 | 0.7359378 | 0.1309046 | 0.7106806 | 0.9826710 | -0.1086357 | 0.5870139 | -0.3184396 | 0.6659132 | -0.1869791 | 0.7962619 |
| GGB9627_SGB15081 | -0.5570538 | 0.0007363 | 0.0025193 | 0.0950715 | 0.5577933 | 0.7881259 | 0.0977297 | 0.6701766 | 0.8835689 | 0.0924132 | 0.6867985 | 0.9931883 | -0.0053165 | 0.9869177 | 0.9948202 | -0.2245717 | 0.4147147 | -0.3545694 | 0.5500289 | -0.3593750 | 0.5442015 |
| GGB9712_SGB15244 | 0.0834814 | 0.6647895 | 0.7737714 | -0.2371537 | 0.2192856 | 0.5213278 | -0.3347496 | 0.2204167 | 0.5796144 | -0.1395578 | 0.6083426 | 0.9931883 | 0.1951917 | 0.6124936 | 0.9826710 | -0.6169049 | 0.1425975 | -0.8721023 | 0.2026031 | -0.6763036 | 0.3971879 |
| GGB9747_SGB15356 | -0.1490394 | 0.5996523 | 0.7155514 | -0.3152190 | 0.2676331 | 0.5802121 | -0.4648212 | 0.2480818 | 0.6211620 | -0.1656168 | 0.6797936 | 0.9931883 | 0.2992044 | 0.5982761 | 0.9826710 | -0.8748132 | 0.2443752 | -1.2566540 | 0.3270115 | -0.9565551 | 0.6253216 |
| GGB9767_SGB15385 | -0.0062842 | 0.9679194 | 0.9782531 | -0.0856220 | 0.5838894 | 0.8025543 | -0.4515128 | 0.0424467 | 0.2500470 | 0.2802689 | 0.2055515 | 0.7316337 | 0.7317818 | 0.0202257 | 0.3378885 | -0.3937033 | 0.2224594 | -0.8874518 | -0.0155739 | -0.1551776 | 0.7157154 |
| GGB9787_SGB15410 | 0.2360569 | 0.2057461 | 0.3193000 | 0.3526064 | 0.0595125 | 0.3339497 | 0.3565285 | 0.1769715 | 0.5128561 | 0.3486844 | 0.1861412 | 0.7241659 | -0.0078441 | 0.9831853 | 0.9948202 | -0.0143073 | 0.7195201 | -0.1626590 | 0.8757159 | -0.1699166 | 0.8672854 |
| GGB9790_SGB15413 | 0.3371675 | 0.0211895 | 0.0497341 | 0.1365694 | 0.3472641 | 0.6848819 | 0.2538239 | 0.2174562 | 0.5771735 | 0.0193148 | 0.9249691 | 1.0000000 | -0.2345091 | 0.4195116 | 0.9815046 | -0.1495240 | 0.4226627 | -0.1510018 | 0.6586496 | -0.3850536 | 0.4236833 |
| Haemophilus_parainfluenzae | 0.0638538 | 0.7535948 | 0.8431227 | 0.4207131 | 0.0398767 | 0.2700392 | 0.3354792 | 0.2447313 | 0.6205685 | 0.5059470 | 0.0798354 | 0.6333906 | 0.1704678 | 0.6752478 | 0.9826710 | 0.0196989 | 0.8217273 | -0.2319609 | 0.9029193 | -0.0608521 | 1.0727462 |
| Intestinibacter_bartlettii | 0.5145710 | 0.0076595 | 0.0205216 | -0.1620575 | 0.3963093 | 0.7078181 | -0.4471369 | 0.0991797 | 0.4022204 | 0.1230218 | 0.6484378 | 0.9931883 | 0.5701587 | 0.1365697 | 0.6639826 | -0.5383330 | 0.2142179 | -0.9795713 | 0.0852975 | -0.4088112 | 0.6548548 |
| Lachnospira_sp_NSJ_43 | -0.7003931 | 0.0015555 | 0.0050777 | 0.3853736 | 0.0784363 | 0.3718112 | 1.1318870 | 0.0003217 | 0.0152257 | -0.3611398 | 0.2420300 | 0.7493886 | -1.4930268 | 0.0007639 | 0.0770871 | -0.0443219 | 0.8150692 | 0.5238625 | 1.7399116 | -0.9684775 | 0.2461980 |
| Lachnospiraceae_bacterium_OM04_12BH | -0.1982599 | 0.4356230 | 0.5675089 | -0.1221019 | 0.6309328 | 0.8165266 | -0.2357325 | 0.5122950 | 0.8070408 | -0.0084713 | 0.9811796 | 1.0000000 | 0.2272611 | 0.6547992 | 0.9826710 | -0.6230419 | 0.3788381 | -0.9445688 | 0.4731039 | -0.7165070 | 0.6995644 |
| Lactococcus_lactis | 0.4473450 | 0.0003578 | 0.0014516 | 0.3209600 | 0.0097287 | 0.1151234 | 0.6419199 | 0.0002972 | 0.0152257 | 0.0000000 | 1.0000000 | 1.0000000 | -0.6419199 | 0.0097287 | 0.2609051 | 0.0787101 | 0.5632099 | 0.2991333 | 0.9847065 | -0.3423994 | 0.3423994 |
| Lentihominibacter_faecis | -0.0313566 | 0.8998784 | 0.9293289 | -0.2603615 | 0.2969755 | 0.6247484 | -0.3249500 | 0.3574471 | 0.6934416 | -0.1957731 | 0.5785471 | 0.9931883 | 0.1291770 | 0.7955319 | 0.9826710 | -0.7517445 | 0.2310214 | -1.0202630 | 0.3703630 | -0.8903007 | 0.4987546 |
| Massilioclostridium_coli | 0.4530499 | 0.0587710 | 0.1151100 | 0.3410670 | 0.1538211 | 0.4779906 | 0.3193175 | 0.3445170 | 0.6904493 | 0.3628164 | 0.2824522 | 0.7788002 | 0.0434989 | 0.9273093 | 0.9826710 | -0.1289750 | 0.8111089 | -0.3457977 | 0.9844327 | -0.3015475 | 1.0271804 |
| Mediterraneibacter_butyricigenes | 0.7943287 | 0.0036954 | 0.0112850 | -0.6048010 | 0.0262544 | 0.2130359 | -0.6006765 | 0.1173645 | 0.4279945 | -0.6089256 | 0.1120486 | 0.6732760 | -0.0082492 | 0.9878144 | 0.9948202 | -1.1372673 | -0.0723348 | -1.3541228 | 0.1527699 | -1.3615210 | 0.1436697 |
| Mediterraneibacter_sp_NSJ_151 | 0.2955616 | 0.0527045 | 0.1054091 | 0.0802774 | 0.5967777 | 0.8025543 | 0.1389126 | 0.5177483 | 0.8079149 | 0.0216422 | 0.9195899 | 1.0000000 | -0.1172705 | 0.6991316 | 0.9826710 | -0.2187776 | 0.3793324 | -0.2842539 | 0.5620792 | -0.4010464 | 0.4443307 |
| Methanobrevibacter_smithii | -0.7057619 | 0.0004010 | 0.0015819 | -0.1525634 | 0.4357187 | 0.7255890 | -0.3434011 | 0.2156819 | 0.5771735 | 0.0382742 | 0.8898662 | 1.0000000 | 0.3816754 | 0.3298237 | 0.9442582 | -0.5381235 | 0.2329966 | -0.8889735 | 0.2021712 | -0.5066819 | 0.5832303 |
| Romboutsia_timonensis | -0.0999055 | 0.6404656 | 0.7547395 | 0.2088686 | 0.3293957 | 0.6634636 | 0.0206706 | 0.9455358 | 0.9973905 | 0.3970667 | 0.1901073 | 0.7296010 | 0.3763960 | 0.3793734 | 0.9699910 | -0.2127460 | 0.6304833 | -0.5759194 | 0.6172607 | -0.1988495 | 0.9929828 |
| Ruminococcus_gnavus | 0.2341570 | 0.3938601 | 0.5301245 | 0.0712007 | 0.7952275 | 0.9001083 | -0.3390500 | 0.3829657 | 0.7153866 | 0.4814514 | 0.2154238 | 0.7316337 | 0.8205014 | 0.1361205 | 0.6639826 | -0.4696635 | 0.6120649 | -1.1043796 | 0.4262795 | -0.2830137 | 1.2459165 |
| Ruminococcus_lactaris | -0.8025082 | 0.0000045 | 0.0000297 | -0.4443154 | 0.0093995 | 0.1151234 | -0.5387120 | 0.0256473 | 0.1867649 | -0.3499189 | 0.1449622 | 0.6749058 | 0.1887931 | 0.5773089 | 0.9826710 | -0.7781084 | -0.1105225 | -1.0110331 | -0.0663908 | -0.8217066 | 0.1218688 |
| Ruminococcus_sp_AF41_9 | -0.1280947 | 0.4991576 | 0.6297176 | 0.3543767 | 0.0627493 | 0.3339497 | 0.3717707 | 0.1666549 | 0.5054071 | 0.3369827 | 0.2092291 | 0.7316337 | -0.0347881 | 0.9268307 | 0.9826710 | -0.0190715 | 0.7278249 | -0.1566632 | 0.9002046 | -0.1908544 | 0.8648197 |
| Senegalimassilia_anaerobia | -0.1985857 | 0.1656382 | 0.2642768 | 0.0764502 | 0.5926054 | 0.8025543 | 0.0898192 | 0.6568114 | 0.8716562 | 0.0630813 | 0.7546960 | 0.9931883 | -0.0267379 | 0.9254210 | 0.9826710 | -0.2051382 | 0.3580387 | -0.3086320 | 0.4882703 | -0.3349198 | 0.4610824 |
| Slackia_isoflavoniconvertens | -0.0910798 | 0.4436485 | 0.5727098 | 0.0524237 | 0.6590762 | 0.8325810 | 0.0213488 | 0.8989345 | 0.9973905 | 0.0834987 | 0.6190959 | 0.9931883 | 0.0621499 | 0.7936509 | 0.9826710 | -0.1817870 | 0.2866345 | -0.3100623 | 0.3527599 | -0.2475381 | 0.4145355 |
| Streptococcus_parasanguinis | 0.1374812 | 0.5864509 | 0.7027513 | 0.2168057 | 0.3912926 | 0.7078181 | 0.0096241 | 0.9785201 | 0.9973905 | 0.4239873 | 0.2360555 | 0.7493886 | 0.4143632 | 0.4126145 | 0.9815046 | -0.2812646 | 0.7148761 | -0.6951517 | 0.7143999 | -0.2799924 | 1.1279671 |
| Veillonella_dispar | 0.1396031 | 0.5349718 | 0.6548793 | -0.0265190 | 0.9061267 | 0.9605496 | -0.0778011 | 0.8068584 | 0.9471457 | 0.0247631 | 0.9379000 | 1.0000000 | 0.1025642 | 0.8196236 | 0.9826710 | -0.4698978 | 0.4168598 | -0.7051876 | 0.5495854 | -0.6019148 | 0.6514409 |
| Victivallis_lenta | 0.7478215 | 0.0000044 | 0.0000297 | 0.1925994 | 0.2229544 | 0.5213278 | 0.1849707 | 0.4075675 | 0.7234323 | 0.2002280 | 0.3695361 | 0.8507175 | 0.0152573 | 0.9614111 | 0.9948202 | -0.1182788 | 0.5034775 | -0.2549258 | 0.6248672 | -0.2391716 | 0.6396277 |
| Bifidobacterium_pseudocatenulatum | 0.1203507 | 0.4836447 | 0.6131924 | 0.2342821 | 0.1736172 | 0.4901612 | 0.2016485 | 0.4070202 | 0.7234323 | 0.2669156 | 0.2722580 | 0.7655571 | 0.0652670 | 0.8492591 | 0.9826710 | -0.1042303 | 0.5727945 | -0.2773507 | 0.6806478 | -0.2115427 | 0.7453738 |
| Eubacterium_sp_AF34_35BH | -0.1732120 | 0.2540260 | 0.3737999 | -0.1079117 | 0.4767816 | 0.7564579 | -0.0853573 | 0.6906771 | 0.8835689 | -0.1304661 | 0.5427090 | 0.9931883 | -0.0451088 | 0.8816972 | 0.9826710 | -0.4067214 | 0.1908981 | -0.5081768 | 0.3374622 | -0.5528080 | 0.2918759 |
| Faecalicatena_contorta | 0.7436050 | 0.0010501 | 0.0035085 | -0.0042480 | 0.9848137 | 0.9882937 | 0.0226852 | 0.9427334 | 0.9973905 | -0.0311811 | 0.9212582 | 1.0000000 | -0.0538663 | 0.9039448 | 0.9826710 | -0.4442737 | 0.4357777 | -0.5999567 | 0.6453271 | -0.6531197 | 0.5907575 |
| GGB9559_SGB14969 | 0.4288588 | 0.0469308 | 0.0952025 | -0.1147603 | 0.5928451 | 0.8025543 | 0.0447283 | 0.8828604 | 0.9871353 | -0.2742489 | 0.3663447 | 0.8507175 | -0.3189773 | 0.4575904 | 0.9815046 | -0.5377301 | 0.3082095 | -0.5537793 | 0.6432359 | -0.8720805 | 0.3235826 |
| GGB9759_SGB15370 | 0.1400843 | 0.3635074 | 0.4987252 | -0.1957374 | 0.2047352 | 0.5145558 | -0.2151215 | 0.3241553 | 0.6856880 | -0.1763534 | 0.4181804 | 0.8926598 | 0.0387681 | 0.8998123 | 0.9826710 | -0.4992994 | 0.1078245 | -0.6446654 | 0.2144225 | -0.6054122 | 0.2527054 |
| Roseburia_lenta | -0.4938826 | 0.0005303 | 0.0019559 | 0.5609384 | 0.0000904 | 0.0064196 | 1.0095993 | 0.0000009 | 0.0002573 | 0.1122776 | 0.5703443 | 0.9931883 | -0.8973217 | 0.0015900 | 0.1128877 | 0.2851084 | 0.8367685 | 0.6192963 | 1.3999023 | -0.2775846 | 0.5021397 |
| Enterocloster_bolteae | -0.2540947 | 0.3145033 | 0.4465947 | -0.2188847 | 0.3860567 | 0.7078181 | -0.4251623 | 0.2345836 | 0.6056523 | -0.0126071 | 0.9717902 | 1.0000000 | 0.4125552 | 0.4139444 | 0.9815046 | -0.7161986 | 0.2784292 | -1.1288677 | 0.2785431 | -0.7155177 | 0.6903034 |
| GGB2848_SGB3813 | -0.0701420 | 0.7780317 | 0.8539447 | 0.2056502 | 0.4089785 | 0.7078181 | 0.8183528 | 0.0211441 | 0.1795889 | -0.4070523 | 0.2480371 | 0.7493886 | -1.2254051 | 0.0146885 | 0.3219095 | -0.2849040 | 0.6962044 | 0.1242125 | 1.5124931 | -1.1004086 | 0.2863040 |
| GGB3005_SGB3996 | -0.2416299 | 0.3228164 | 0.4516249 | 0.3248668 | 0.1842923 | 0.4996872 | 0.5071605 | 0.1432236 | 0.4616646 | 0.1425730 | 0.6794197 | 0.9931883 | -0.3645876 | 0.4554351 | 0.9815046 | -0.1562707 | 0.8060042 | -0.1736549 | 1.1879760 | -0.5374735 | 0.8226195 |
| GGB3061_SGB4063 | -0.3720429 | 0.0205384 | 0.0489740 | 0.0578505 | 0.7165169 | 0.8659182 | 0.2082176 | 0.3562149 | 0.6934416 | -0.0925166 | 0.6811945 | 0.9931883 | -0.3007342 | 0.3458221 | 0.9442582 | -0.2562041 | 0.3719051 | -0.2361736 | 0.6526088 | -0.5364058 | 0.3513726 |
| GGB36331_SGB15121 | -0.1610729 | 0.2037593 | 0.3179541 | -0.1722296 | 0.1743179 | 0.4901612 | -0.3702019 | 0.0397876 | 0.2446731 | 0.0257426 | 0.8854516 | 1.0000000 | 0.3959445 | 0.1187410 | 0.6535935 | -0.4214907 | 0.0770314 | -0.7229094 | -0.0174944 | -0.3265665 | 0.3780517 |
| Hungatella_hathewayi | 0.3805706 | 0.1354893 | 0.2224218 | 0.0637994 | 0.8017398 | 0.9035480 | 0.1111378 | 0.7572433 | 0.9190474 | 0.0164610 | 0.9634372 | 1.0000000 | -0.0946767 | 0.8521951 | 0.9826710 | -0.4371209 | 0.5647197 | -0.5976708 | 0.8199463 | -0.6915469 | 0.7244689 |
| TM7_phylum_sp_oral_taxon_352 | 0.2211431 | 0.3533003 | 0.4870742 | 0.5046715 | 0.0351570 | 0.2560152 | 0.5483149 | 0.1048039 | 0.4022204 | 0.4610281 | 0.1716418 | 0.6963755 | -0.0872868 | 0.8544685 | 0.9826710 | 0.0355516 | 0.9737914 | -0.1154956 | 1.2121254 | -0.2020326 | 1.1240888 |
| Veillonella_parvula | 0.4135441 | 0.0921216 | 0.1605064 | 0.5392612 | 0.0285481 | 0.2252126 | 0.6173761 | 0.0757108 | 0.3468043 | 0.4611464 | 0.1831797 | 0.7225423 | -0.1562297 | 0.7493454 | 0.9826710 | 0.0572857 | 1.0212368 | -0.0646253 | 1.2993775 | -0.2200847 | 1.1423775 |
| GGB6649_SGB9391 | 0.1669050 | 0.2297361 | 0.3433950 | 0.0923399 | 0.5057295 | 0.7827994 | -0.1074148 | 0.5842290 | 0.8281574 | 0.2920945 | 0.1374522 | 0.6749058 | 0.3995093 | 0.1509900 | 0.6692687 | -0.1810464 | 0.3657261 | -0.4942597 | 0.2794301 | -0.0943134 | 0.6785025 |
| Veillonella_atypica | 0.2057969 | 0.3028862 | 0.4322597 | 0.1782601 | 0.3719781 | 0.7078181 | 0.2997149 | 0.2890230 | 0.6783679 | 0.0568054 | 0.8402928 | 1.0000000 | -0.2429095 | 0.5427369 | 0.9826710 | -0.2149378 | 0.5714580 | -0.2566651 | 0.8560948 | -0.4989461 | 0.6125569 |
Open code
if(file.exists('gitignore/result_microbiome.csv') == FALSE){
write.table(result_microbiome, 'gitignore/result_microbiome.csv', row.names = FALSE)
}5 Elastic net
To assess the predictive power of microbiome features to discriminate between diet strategy, we employed Elastic Net logistic regression.
As we expected very high level of co-linearity, we allowed \(alpha\) to rather small (0, 0.2 or 0.4). All features were standardized by 2 standard deviations.
The performance of the predictive models was evaluated through their capacity of discriminate between vegan and omnivore diets, using out-of-sample area under ROC curve (AUC; estimated with out-of-bag bootstrap) as the measure of discriminatory capacity.
All features were transformed by 2 standard deviations (resulting in standard deviation of 0.5).
5.1 Prepare data for glmnet
Open code
data_microbiome_glmnet <- data_microbiome_original %>%
na.omit() %>%
dplyr::mutate(
vegan = as.numeric(
dplyr::if_else(
Diet == "VEGAN", 1, 0
)
),
dplyr::across(
`Adlercreutzia_equolifaciens`:`Veillonella_atypica`, ~ arm::rescale(.)
)
) %>%
dplyr::select(
vegan,
dplyr::everything()
) %>%
dplyr::select(
Sample, vegan, `Adlercreutzia_equolifaciens`:`Veillonella_atypica`
)5.2 Fit model
Open code
modelac <- "elanet_microbiome_all"
assign(
modelac,
run(
expr = clust_glmnet(
data = data_microbiome_glmnet,
outcome = "vegan",
clust_id = "Sample",
sample_method = "oos_boot",
N = 500,
alphas = c(0, 0.2, 0.4),
family = "binomial",
seed = 478
),
path = paste0("gitignore/run/", modelac)
)
)5.3 Model summary
Open code
elanet_microbiome_all$model_summary
## alpha lambda auc auc_OutOfSample auc_oos_CIL auc_oos_CIU accuracy
## 1 0.4 0.05671541 0.9867025 0.8202338 0.7314971 0.9017181 0.9216867
## accuracy_OutOfSample accuracy_oos_CIL accuracy_oos_CIU
## 1 0.7374451 0.6349206 0.83199155.4 Calibration plot
Open code
elanet_microbiome_all$plot
5.5 Estimated coefficients
Open code
data.frame(
microbiome = row.names(
elanet_microbiome_all$betas
)[
which(
abs(
elanet_microbiome_all$betas
)>0
)
],
beta = elanet_microbiome_all$betas[
abs(
elanet_microbiome_all$betas
)>0
]
) %>%
mutate(
is_in_ExtValCoh = if_else(
microbiome %in% names(data_microbiome_validation),
1, 0
)
)
## microbiome beta is_in_ExtValCoh
## 1 (Intercept) 0.407222882 0
## 2 Agathobaculum_butyriciproducens 0.621419023 1
## 3 Anaerofilum_hominis 0.084631010 1
## 4 Anaerotignum_faecicola -0.193830429 1
## 5 Anaerotruncus_colihominis 0.093112698 1
## 6 Bacteroides_ovatus 0.024651413 1
## 7 Barnesiella_intestinihominis -0.095395373 1
## 8 Brotolimicola_acetigignens 0.054915462 1
## 9 Clostridia_bacterium_UC5_1_1D1 0.082518832 1
## 10 Clostridium_fessum -0.417582156 1
## 11 Collinsella_aerofaciens -0.207051433 1
## 12 Coprobacter_fastidiosus 0.145557806 1
## 13 Coprococcus_comes -0.063292251 1
## 14 Dysosmobacter_welbionis -0.064305792 1
## 15 Enterocloster_hominis -0.031824969 1
## 16 Escherichia_coli -0.300300259 1
## 17 Eubacterium_ramulus -0.046621505 1
## 18 GGB2653_SGB3574 0.213516163 1
## 19 GGB3034_SGB4030 0.111313257 1
## 20 GGB33586_SGB53517 -0.004922735 1
## 21 GGB38744_SGB14842 0.317900636 1
## 22 GGB9730_SGB15291 -0.040034023 1
## 23 GGB9775_SGB15395 -0.154920380 1
## 24 Guopingia_tenuis 0.210530302 1
## 25 Hydrogenoanaerobacterium_saccharovorans -0.186637026 1
## 26 Lachnoclostridium_sp_An138 0.010127428 1
## 27 Lachnospiraceae_bacterium 0.015302230 1
## 28 Lachnospiraceae_bacterium_CLA_AA_H215 -0.175695733 1
## 29 Lachnospiraceae_bacterium_CLA_AA_H244 -0.018895954 1
## 30 Lawsonibacter_asaccharolyticus -0.280783573 1
## 31 Ligaoa_zhengdingensis 0.081559857 1
## 32 Phocaeicola_dorei -0.047287220 1
## 33 Provencibacterium_massiliense 0.071582126 1
## 34 Roseburia_hominis 0.304585688 1
## 35 Ruthenibacterium_lactatiformans -0.113547383 1
## 36 Vescimonas_coprocola -0.015309680 1
## 37 Youxingia_wuxianensis 0.040315222 1
## 38 bacterium_210917_DFI_7_65 -0.010704440 1
## 39 GGB9708_SGB15233 0.221034267 1
## 40 GGB9760_SGB15374 -0.001830135 1
## 41 Segatella_brunsvicensis -0.076221089 1
## 42 Clostridiaceae_bacterium_Marseille_Q4149 -0.192744400 1
## 43 GGB2970_SGB3952 -0.016739447 1
## 44 GGB9787_SGB15410 0.016549069 1
## 45 Haemophilus_parainfluenzae 0.089464351 1
## 46 Lactococcus_lactis 0.021571531 1
## 47 Mediterraneibacter_butyricigenes -0.124738294 1
## 48 Ruminococcus_lactaris -0.066841896 1
## 49 Roseburia_lenta 0.245591876 1
## 50 TM7_phylum_sp_oral_taxon_352 0.053481028 1
## 51 Veillonella_parvula 0.003324881 1
elanet_microbiome_all$betas
## 285 x 1 sparse Matrix of class "dgCMatrix"
## s0
## (Intercept) 0.407222882
## Adlercreutzia_equolifaciens .
## Agathobaculum_butyriciproducens 0.621419023
## Akkermansia_muciniphila .
## Alistipes_communis .
## Alistipes_finegoldii .
## Alistipes_ihumii .
## Alistipes_indistinctus .
## Alistipes_onderdonkii .
## Alistipes_putredinis .
## Alistipes_senegalensis .
## Alistipes_shahii .
## Anaerobutyricum_hallii .
## Anaerofilum_hominis 0.084631010
## Anaeromassilibacillus_senegalensis .
## Anaerostipes_hadrus .
## Anaerotignum_faecicola -0.193830429
## Anaerotruncus_colihominis 0.093112698
## Anaerotruncus_massiliensis .
## Anaerotruncus_rubiinfantis .
## Bacteroides_caccae .
## Bacteroides_cellulosilyticus .
## Bacteroides_clarus .
## Bacteroides_eggerthii .
## Bacteroides_fragilis .
## Bacteroides_ovatus 0.024651413
## Bacteroides_stercoris .
## Bacteroides_thetaiotaomicron .
## Bacteroides_uniformis .
## Bacteroides_xylanisolvens .
## Barnesiella_intestinihominis -0.095395373
## Bifidobacterium_adolescentis .
## Bifidobacterium_longum .
## Bilophila_SGB15451 .
## Bilophila_wadsworthia .
## Blautia_faecis .
## Blautia_glucerasea .
## Blautia_massiliensis .
## Blautia_obeum .
## Blautia_sp_MCC283 .
## Blautia_wexlerae .
## Brotolimicola_acetigignens 0.054915462
## Butyricimonas_faecihominis .
## Butyricimonas_virosa .
## Candidatus_Borkfalkia_ceftriaxoniphila .
## Candidatus_Cibionibacter_quicibialis .
## Clostridia_bacterium_UC5_1_1D1 0.082518832
## Clostridiaceae_bacterium .
## Clostridiaceae_bacterium_AF18_31LB .
## Clostridiaceae_bacterium_Marseille_Q4143 .
## Clostridiaceae_bacterium_Marseille_Q4145 .
## Clostridiales_bacterium .
## Clostridiales_bacterium_KLE1615 .
## Clostridium_SGB4750 .
## Clostridium_SGB4909 .
## Clostridium_fessum -0.417582156
## Clostridium_leptum .
## Clostridium_sp_AF20_17LB .
## Clostridium_sp_AF27_2AA .
## Clostridium_sp_AF36_4 .
## Clostridium_sp_AM22_11AC .
## Clostridium_sp_AM33_3 .
## Collinsella_aerofaciens -0.207051433
## Coprobacter_fastidiosus 0.145557806
## Coprococcus_catus .
## Coprococcus_comes -0.063292251
## Coprococcus_eutactus .
## Dorea_formicigenerans .
## Dorea_longicatena .
## Dorea_sp_AF36_15AT .
## Dysosmobacter_SGB15077 .
## Dysosmobacter_welbionis -0.064305792
## Eggerthella_lenta .
## Enterocloster_citroniae .
## Enterocloster_hominis -0.031824969
## Escherichia_coli -0.300300259
## Eubacterium_ramulus -0.046621505
## Eubacterium_rectale .
## Eubacterium_siraeum .
## Eubacterium_ventriosum .
## Faecalibacterium_SGB15346 .
## Faecalibacterium_prausnitzii .
## Faecalibacterium_sp_CLA_AA_H233 .
## Faecalibacterium_sp_HTFF .
## Faecalicatena_fissicatena .
## Flavonifractor_plautii .
## Fusicatenibacter_saccharivorans .
## Fusicatenibacter_sp_CLA_AA_H277 .
## GGB13404_SGB14252 .
## GGB1420_SGB1957 .
## GGB2653_SGB3574 0.213516163
## GGB2998_SGB3988 .
## GGB3034_SGB4030 0.111313257
## GGB3109_SGB4121 .
## GGB3175_SGB4191 .
## GGB33469_SGB15236 .
## GGB33512_SGB15203 .
## GGB33586_SGB53517 -0.004922735
## GGB3537_SGB4727 .
## GGB38744_SGB14842 0.317900636
## GGB45432_SGB63101 .
## GGB45613_SGB63326 .
## GGB47687_SGB2286 .
## GGB52106_SGB72838 .
## GGB52130_SGB14966 .
## GGB9062_SGB13981 .
## GGB9063_SGB13982 .
## GGB9064_SGB13983 .
## GGB9342_SGB14306 .
## GGB9345_SGB14311 .
## GGB9453_SGB14844 .
## GGB9502_SGB14899 .
## GGB9509_SGB14906 .
## GGB9522_SGB14921 .
## GGB9531_SGB14932 .
## GGB9534_SGB14937 .
## GGB9602_SGB15031 .
## GGB9614_SGB15049 .
## GGB9619_SGB15067 .
## GGB9621_SGB15073 .
## GGB9635_SGB15106 .
## GGB9646_SGB15123 .
## GGB9667_SGB15164 .
## GGB9699_SGB15216 .
## GGB9708_SGB15234 .
## GGB9715_SGB15265 .
## GGB9719_SGB15272 .
## GGB9719_SGB15273 .
## GGB9730_SGB15291 -0.040034023
## GGB9758_SGB15368 .
## GGB9760_SGB15373 .
## GGB9765_SGB15382 .
## GGB9770_SGB15390 .
## GGB9775_SGB15395 -0.154920380
## GGB9781_SGB15402 .
## GGB9818_SGB15459 .
## Gemmiger_formicilis .
## Guopingia_tenuis 0.210530302
## Holdemania_filiformis .
## Hydrogenoanaerobacterium_saccharovorans -0.186637026
## Intestinimonas_butyriciproducens .
## Intestinimonas_gabonensis .
## Intestinimonas_massiliensis .
## Lachnoclostridium_sp_An138 0.010127428
## Lachnospira_eligens .
## Lachnospira_pectinoschiza .
## Lachnospiraceae_bacterium 0.015302230
## Lachnospiraceae_bacterium_AM48_27BH .
## Lachnospiraceae_bacterium_CLA_AA_H215 -0.175695733
## Lachnospiraceae_bacterium_CLA_AA_H244 -0.018895954
## Lachnotalea_sp_AF33_28 .
## Lacrimispora_amygdalina .
## Lawsonibacter_SGB15145 .
## Lawsonibacter_asaccharolyticus -0.280783573
## Lawsonibacter_hominis .
## Ligaoa_zhengdingensis 0.081559857
## Mediterraneibacter_faecis .
## Odoribacter_splanchnicus .
## Oliverpabstia_intestinalis .
## Oscillibacter_sp_ER4 .
## Oscillibacter_sp_MSJ_31 .
## Oscillibacter_sp_PC13 .
## Oscillibacter_valericigenes .
## Oscillospiraceae_bacterium .
## Oscillospiraceae_bacterium_CLA_AA_H250 .
## Oscillospiraceae_bacterium_Marseille_Q3528 .
## Parabacteroides_distasonis .
## Parabacteroides_merdae .
## Paraprevotella_clara .
## Parasutterella_excrementihominis .
## Phascolarctobacterium_faecium .
## Phocaeicola_dorei -0.047287220
## Phocaeicola_sartorii .
## Phocaeicola_vulgatus .
## Phocea_massiliensis .
## Provencibacterium_massiliense 0.071582126
## Pseudoflavonifractor_capillosus .
## Roseburia_faecis .
## Roseburia_hominis 0.304585688
## Roseburia_intestinalis .
## Roseburia_inulinivorans .
## Ruminococcus_bicirculans .
## Ruminococcus_bromii .
## Ruminococcus_torques .
## Ruthenibacterium_lactatiformans -0.113547383
## Segatella_copri .
## Simiaoa_sunii .
## Streptococcus_salivarius .
## Streptococcus_thermophilus .
## Sutterella_wadsworthensis .
## Vescimonas_coprocola -0.015309680
## Wansuia_hejianensis .
## Youxingia_wuxianensis 0.040315222
## bacterium_210917_DFI_7_65 -0.010704440
## Bacteroides_faecis .
## Clostridiaceae_unclassified_SGB4771 .
## Clostridium_sp_AM49_4BH .
## Colidextribacter_sp_210702_DFI_3_9 .
## Enterocloster_lavalensis .
## GGB2982_SGB3964 .
## GGB3304_SGB4367 .
## GGB3619_SGB4894 .
## GGB9296_SGB14253 .
## GGB9524_SGB14924 .
## GGB9574_SGB14987 .
## GGB9619_SGB15066 .
## GGB9707_SGB15229 .
## GGB9708_SGB15233 0.221034267
## GGB9760_SGB15374 -0.001830135
## Roseburia_sp_AF02_12 .
## Segatella_brunsvicensis -0.076221089
## Wujia_chipingensis .
## Alistipes_dispar .
## Alistipes_sp_AF17_16 .
## Anaerobutyricum_soehngenii .
## Anaerosacchariphilus_sp_NSJ_68 .
## Anaerotignum_sp_MSJ_24 .
## Bittarella_massiliensis .
## Blautia_SGB4815 .
## Blautia_luti .
## Blautia_sp_OF03_15BH .
## Butyricimonas_paravirosa .
## Catenibacillus_scindens .
## Clostridiaceae_bacterium_Marseille_Q4149 -0.192744400
## Clostridium_SGB6173 .
## Clostridium_SGB6179 .
## Clostridium_sp_Marseille_P3244 .
## Clostridium_sp_NSJ_42 .
## Coprobacter_secundus .
## Eubacteriaceae_bacterium .
## Faecalibacillus_faecis .
## Faecalibacillus_intestinalis .
## GGB13489_SGB15224 .
## GGB2970_SGB3952 -0.016739447
## GGB3352_SGB4436 .
## GGB34797_SGB14322 .
## GGB34900_SGB14891 .
## GGB3653_SGB4964 .
## GGB4456_SGB6141 .
## GGB4552_SGB6276 .
## GGB51441_SGB71759 .
## GGB58158_SGB79798 .
## GGB9365_SGB14341 .
## GGB9412_SGB14770 .
## GGB9627_SGB15081 .
## GGB9712_SGB15244 .
## GGB9747_SGB15356 .
## GGB9767_SGB15385 .
## GGB9787_SGB15410 0.016549069
## GGB9790_SGB15413 .
## Haemophilus_parainfluenzae 0.089464351
## Intestinibacter_bartlettii .
## Lachnospira_sp_NSJ_43 .
## Lachnospiraceae_bacterium_OM04_12BH .
## Lactococcus_lactis 0.021571531
## Lentihominibacter_faecis .
## Massilioclostridium_coli .
## Mediterraneibacter_butyricigenes -0.124738294
## Mediterraneibacter_sp_NSJ_151 .
## Methanobrevibacter_smithii .
## Romboutsia_timonensis .
## Ruminococcus_gnavus .
## Ruminococcus_lactaris -0.066841896
## Ruminococcus_sp_AF41_9 .
## Senegalimassilia_anaerobia .
## Slackia_isoflavoniconvertens .
## Streptococcus_parasanguinis .
## Veillonella_dispar .
## Victivallis_lenta .
## Bifidobacterium_pseudocatenulatum .
## Eubacterium_sp_AF34_35BH .
## Faecalicatena_contorta .
## GGB9559_SGB14969 .
## GGB9759_SGB15370 .
## Roseburia_lenta 0.245591876
## Enterocloster_bolteae .
## GGB2848_SGB3813 .
## GGB3005_SGB3996 .
## GGB3061_SGB4063 .
## GGB36331_SGB15121 .
## Hungatella_hathewayi .
## TM7_phylum_sp_oral_taxon_352 0.053481028
## Veillonella_parvula 0.003324881
## GGB6649_SGB9391 .
## Veillonella_atypica .5.6 Plot beta coefficients
Open code
data.frame(
microbiome = row.names(elanet_microbiome_all$betas),
beta = elanet_microbiome_all$betas[, 1]
) %>%
arrange(abs(beta)) %>%
filter(abs(beta) > 0,
!grepl('Intercept', microbiome)) %>%
mutate(microbiome = factor(microbiome, levels = microbiome)) %>% # Preserve order
ggplot(
aes(
x = microbiome,
y = beta
)
) +
geom_point() +
geom_hline(yintercept = 0, color = "black") +
labs(
y = "Standardized beta coefficients",
x = "Bacteria species"
) +
theme_minimal() +
coord_flip() + # Flip coordinates to have outcomes on the y-axis
theme(
axis.text.x = element_text(size = 10),
axis.text.y = element_text(size = 10),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
legend.position = "bottom"
)
6 External validation
External validation was performed with an independent Czech cohort.
As a first step, we will use the previously developed and validated elastic net model to predict vegan status in the independent Czech cohort. The validation data will be standardized using the mean and standard deviation of each taxa as taken from the training cohort to ensure comparability across datasets. For each subject in the external validation cohort, we will estimate the predicted probability of being vegan using the elastic net model. This predicted probability will then be used as a variable to discriminate between the diet groups in the independent cohort.
In a 2nd step, we will look at taxa that significantly differed between diet groups (average vegan diet effect across both countries, FDR<0.01) estimated by linear models (one per a taxa) with data of training cohort. Then we will fit linear models also for external validation cohort. Effect of vegan diet on these taxa will be shown along with 95% confidence interval for all cohorts: training Czech and Italian cohorts, but also in Czech independent (validating) cohort
6.1 Prediction of diet (elastic net)
6.1.1 Get table of weights, means and SDs
Open code
coefs_microbiome_all <- get_coef(
original_data = data_analysis,
glmnet_model = elanet_microbiome_all)
coefs_microbiome_all
## # A tibble: 285 × 5
## predictor beta_scaled beta_OrigScale mean SD
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 (Intercept) 0.407 NA NA NA
## 2 Adlercreutzia_equolifaciens 0 0 -0.936 1.48
## 3 Agathobaculum_butyriciproducens 0.621 1.30 1.63 1.04
## 4 Akkermansia_muciniphila 0 0 1.44 2.26
## 5 Alistipes_communis 0 0 1.67 1.78
## 6 Alistipes_finegoldii 0 0 0.888 1.87
## 7 Alistipes_ihumii 0 0 0.838 1.49
## 8 Alistipes_indistinctus 0 0 -0.0519 1.48
## 9 Alistipes_onderdonkii 0 0 1.83 2.40
## 10 Alistipes_putredinis 0 0 2.96 2.72
## # ℹ 275 more rows6.1.3 Standardize data in validation set
Open code
data_microbiome_validation_pred_all <- data_microbiome_validation %>%
dplyr::mutate(
vegan = if_else(
Diet == "VEGAN", 1, 0
)
) %>%
dplyr::select(
vegan,
dplyr::all_of(common_predictors)
) %>%
dplyr::mutate(
across(
.cols = -vegan,
.fns = ~ .
- coefs_microbiome_all$mean[
match(
cur_column(),
coefs_microbiome_all$predictor
)
]
)
) %>%
dplyr::mutate(
across(
.cols = -vegan,
.fns = ~ .
/ coefs_microbiome_all$SD[
match(
cur_column(),
coefs_microbiome_all$predictor
)
]
)
) 6.1.4 Result
Open code
elanet_microbiome_all$fit
##
## Call: glmnet::glmnet(x = original_predictors, y = original_outcome, family = family, alpha = optim_par$alpha[1], lambda = optim_par$lamb_1se[1], standardize = standardize)
##
## Df %Dev Lambda
## 1 50 40.65 0.05672
newx <- as.matrix(data_microbiome_validation_pred_all[,-1])
predicted <- predict(
elanet_microbiome_all$fit,
newx = newx)
tr <- data_microbiome_validation_pred_all %>%
dplyr::mutate(
predicted_logit = as.numeric(
predict(
elanet_microbiome_all$fit,
newx = newx
)
)
) %>%
dplyr::mutate(
predicted = inv_logit(predicted_logit)
)
roc_microbiome_all <- pROC::roc(
vegan ~ predicted_logit,
data = tr,
direction = "<",
levels = c(0, 1),
ci = TRUE
)
roc_microbiome_all
##
## Call:
## roc.formula(formula = vegan ~ predicted_logit, data = tr, direction = "<", levels = c(0, 1), ci = TRUE)
##
## Data: predicted_logit in 43 controls (vegan 0) < 58 cases (vegan 1).
## Area under the curve: 0.8372
## 95% CI: 0.7584-0.916 (DeLong)
plot(roc_microbiome_all)
6.2 Diet effect across datasets
Similarly as in training data cohorts, we will fit linear model per each of the selected taxa (\(CLR\) - transformed), with a single fixed effect factor of diet.
6.2.1 Linear models in validation cohort
Open code
data_analysis_microbiome <- data_microbiome_validation %>%
dplyr::mutate(
Diet_VEGAN = as.numeric(
dplyr::if_else(
Diet == 'VEGAN', 1, 0
)
)
) %>%
dplyr::select(
Diet_VEGAN,
all_of(common_microbiome)
)6.2.1.1 Define number of microbiome and covariates
Open code
n_covarites <- 1
n_features <- ncol(data_analysis_microbiome) - n_covarites6.2.1.2 Create empty objects
Open code
outcome <- vector('double', n_features)
logFD_VGdiet <- vector('double', n_features)
P_VGdiet <- vector('double', n_features)
CI_L_VGdiet <- vector('double', n_features)
CI_U_VGdiet <- vector('double', n_features)6.2.1.3 Estimate over outcomes
Open code
for (i in 1:n_features) {
## define variable
data_analysis_microbiome$outcome <- data_analysis_microbiome[, (i + n_covarites)]
## fit model
model <- lm(outcome ~ Diet_VEGAN, data = data_analysis_microbiome)
## save results
outcome[i] <- names(data_analysis_microbiome)[i + n_covarites]
## diet effect
tr <- confint(model)
CI_L_VGdiet[i] <- tr[which(row.names(tr) == "Diet_VEGAN"), ][1]
CI_U_VGdiet[i] <- tr[which(row.names(tr) == "Diet_VEGAN"), ][2]
logFD_VGdiet[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Diet_VEGAN"
), 1
]
P_VGdiet[i] <- summary(model)$coefficients[
which(
names(model$coefficients) == "Diet_VEGAN"
), 4
]
}6.2.1.4 Results table
Open code
result_microbiome_val <- data.frame(
outcome,
logFD_VGdiet, P_VGdiet,
CI_L_VGdiet, CI_U_VGdiet
)
kableExtra::kable(result_microbiome_val,
caption = "Results of linear models estimating the effect of diet on CLR-trasformed taxa count. Only lipids that significantly differed between diet groups in training cohorts (FDR < 0.1, average effect across both training cohorts) were included. `logFD` represents the estimated effects (regression coefficient), indicating how much the CLR-transformed taxa count differ between vegans and omnivores. `P`: p-value, `fdr`: p-value adjusted for multiple comparisons, and `CI_L` and `CI_U` represent the lower and upper bounds of the 95% confidence interval, respectively. All estimates in a single row are based on a single model."
)| outcome | logFD_VGdiet | P_VGdiet | CI_L_VGdiet | CI_U_VGdiet |
|---|---|---|---|---|
| Adlercreutzia_equolifaciens | -0.1712072 | 0.4895466 | -0.6609763 | 0.3185619 |
| Agathobaculum_butyriciproducens | 0.5537807 | 0.0008637 | 0.2340022 | 0.8735593 |
| Akkermansia_muciniphila | -0.1277027 | 0.7334571 | -0.8697112 | 0.6143058 |
| Alistipes_communis | -0.0188421 | 0.9380698 | -0.4988149 | 0.4611307 |
| Alistipes_finegoldii | -0.2539928 | 0.4124540 | -0.8663162 | 0.3583306 |
| Alistipes_ihumii | 0.5023615 | 0.0218233 | 0.0745966 | 0.9301264 |
| Alistipes_indistinctus | 0.2501329 | 0.4332701 | -0.3806615 | 0.8809272 |
| Alistipes_onderdonkii | 0.2929591 | 0.3125723 | -0.2797356 | 0.8656537 |
| Alistipes_putredinis | -0.4535196 | 0.2490353 | -1.2296037 | 0.3225646 |
| Alistipes_senegalensis | 0.1223145 | 0.5738555 | -0.3078061 | 0.5524352 |
| Alistipes_shahii | 0.1102602 | 0.6246611 | -0.3355110 | 0.5560314 |
| Anaerobutyricum_hallii | -0.1045680 | 0.6387499 | -0.5451855 | 0.3360494 |
| Anaerofilum_hominis | 1.0367586 | 0.0173732 | 0.1864692 | 1.8870479 |
| Anaeromassilibacillus_senegalensis | -0.0320458 | 0.9302484 | -0.7566266 | 0.6925350 |
| Anaerostipes_hadrus | 0.2206812 | 0.1562736 | -0.0858334 | 0.5271958 |
| Anaerotignum_faecicola | -0.5252774 | 0.0274779 | -0.9910399 | -0.0595148 |
| Anaerotruncus_colihominis | -0.7721826 | 0.0133008 | -1.3799612 | -0.1644040 |
| Anaerotruncus_massiliensis | 0.2777109 | 0.1667675 | -0.1178920 | 0.6733138 |
| Anaerotruncus_rubiinfantis | 0.9606116 | 0.0070677 | 0.2677258 | 1.6534974 |
| Bacteroides_caccae | -0.1387429 | 0.5256803 | -0.5710077 | 0.2935220 |
| Bacteroides_cellulosilyticus | 0.5612561 | 0.0519699 | -0.0048823 | 1.1273944 |
| Bacteroides_clarus | -0.1340533 | 0.3263691 | -0.4037269 | 0.1356203 |
| Bacteroides_eggerthii | -0.1177902 | 0.6885696 | -0.6992239 | 0.4636435 |
| Bacteroides_fragilis | -0.0775871 | 0.7252147 | -0.5143274 | 0.3591531 |
| Bacteroides_ovatus | 0.6884843 | 0.0113963 | 0.1586691 | 1.2182996 |
| Bacteroides_stercoris | -0.3655674 | 0.1282080 | -0.8384118 | 0.1072769 |
| Bacteroides_thetaiotaomicron | 0.1316828 | 0.6434847 | -0.4311276 | 0.6944933 |
| Bacteroides_uniformis | -0.2030937 | 0.4686614 | -0.7570518 | 0.3508643 |
| Bacteroides_xylanisolvens | 0.3189791 | 0.3004004 | -0.2890032 | 0.9269613 |
| Barnesiella_intestinihominis | -0.6391749 | 0.0045553 | -1.0760364 | -0.2023135 |
| Bifidobacterium_adolescentis | 0.6577163 | 0.0545191 | -0.0129987 | 1.3284313 |
| Bifidobacterium_longum | 0.7509240 | 0.0024420 | 0.2718638 | 1.2299841 |
| Bilophila_SGB15451 | -0.0646024 | 0.2053893 | -0.1651612 | 0.0359564 |
| Bilophila_wadsworthia | 0.2377731 | 0.3187289 | -0.2330223 | 0.7085684 |
| Blautia_faecis | -0.0867731 | 0.6701776 | -0.4898292 | 0.3162831 |
| Blautia_glucerasea | -0.4687770 | 0.0434679 | -0.9235313 | -0.0140228 |
| Blautia_massiliensis | -0.6766600 | 0.0134021 | -1.2098558 | -0.1434643 |
| Blautia_obeum | -0.1130708 | 0.6471065 | -0.6016671 | 0.3755254 |
| Blautia_sp_MCC283 | 0.3521311 | 0.2594842 | -0.2639469 | 0.9682091 |
| Blautia_wexlerae | -0.2687129 | 0.0377658 | -0.5219303 | -0.0154955 |
| Brotolimicola_acetigignens | -0.6579227 | 0.0453567 | -1.3019769 | -0.0138685 |
| Butyricimonas_faecihominis | 0.2836388 | 0.1439125 | -0.0984288 | 0.6657063 |
| Butyricimonas_virosa | 0.1704732 | 0.1459978 | -0.0603651 | 0.4013115 |
| Candidatus_Borkfalkia_ceftriaxoniphila | 0.0508793 | 0.8424411 | -0.4556856 | 0.5574443 |
| Candidatus_Cibionibacter_quicibialis | -0.2883849 | 0.1897526 | -0.7217588 | 0.1449889 |
| Clostridia_bacterium_UC5_1_1D1 | -0.3502745 | 0.3140671 | -1.0371424 | 0.3365933 |
| Clostridiaceae_bacterium | 0.2940025 | 0.1167047 | -0.0746116 | 0.6626167 |
| Clostridiaceae_bacterium_AF18_31LB | -0.2764914 | 0.0301573 | -0.5259015 | -0.0270813 |
| Clostridiaceae_bacterium_Marseille_Q4143 | -0.1494612 | 0.2024401 | -0.3805852 | 0.0816627 |
| Clostridiaceae_bacterium_Marseille_Q4145 | 0.3719162 | 0.0296333 | 0.0375238 | 0.7063085 |
| Clostridiales_bacterium | 0.2111988 | 0.4089236 | -0.2941174 | 0.7165149 |
| Clostridiales_bacterium_KLE1615 | 0.2199507 | 0.2351468 | -0.1454236 | 0.5853250 |
| Clostridium_SGB4750 | 0.0675850 | 0.7080028 | -0.2894331 | 0.4246030 |
| Clostridium_SGB4909 | 0.5328757 | 0.1363158 | -0.1711445 | 1.2368959 |
| Clostridium_fessum | -0.3313288 | 0.0327545 | -0.6349262 | -0.0277315 |
| Clostridium_leptum | 0.9120195 | 0.0053713 | 0.2763156 | 1.5477234 |
| Clostridium_sp_AF20_17LB | 0.3906820 | 0.0805226 | -0.0483397 | 0.8297037 |
| Clostridium_sp_AF27_2AA | 0.7160025 | 0.0009135 | 0.3004896 | 1.1315155 |
| Clostridium_sp_AF36_4 | -0.4404313 | 0.1702251 | -1.0729976 | 0.1921350 |
| Clostridium_sp_AM22_11AC | 0.0384912 | 0.8289564 | -0.3140973 | 0.3910798 |
| Clostridium_sp_AM33_3 | 0.1253889 | 0.3773539 | -0.1551798 | 0.4059577 |
| Collinsella_aerofaciens | -0.0748634 | 0.8080372 | -0.6846304 | 0.5349036 |
| Coprobacter_fastidiosus | 0.4436160 | 0.0610310 | -0.0209238 | 0.9081557 |
| Coprococcus_catus | -0.4613416 | 0.0012003 | -0.7357998 | -0.1868834 |
| Coprococcus_comes | -1.0673442 | 0.0000000 | -1.3713852 | -0.7633031 |
| Coprococcus_eutactus | 0.4381462 | 0.3634368 | -0.5140267 | 1.3903190 |
| Dorea_formicigenerans | -0.4849885 | 0.0000141 | -0.6955631 | -0.2744139 |
| Dorea_longicatena | -0.7243893 | 0.0000019 | -1.0080790 | -0.4406996 |
| Dorea_sp_AF36_15AT | -0.2449941 | 0.1043677 | -0.5415733 | 0.0515851 |
| Dysosmobacter_SGB15077 | -0.3991065 | 0.0441083 | -0.7874769 | -0.0107360 |
| Dysosmobacter_welbionis | -0.3426355 | 0.2319397 | -0.9078904 | 0.2226193 |
| Eggerthella_lenta | -0.4342056 | 0.1261006 | -0.9926894 | 0.1242782 |
| Enterocloster_citroniae | -0.1039522 | 0.7343712 | -0.7101222 | 0.5022177 |
| Enterocloster_hominis | 0.5173151 | 0.0581160 | -0.0181277 | 1.0527578 |
| Escherichia_coli | 0.0267410 | 0.9252341 | -0.5372348 | 0.5907169 |
| Eubacterium_ramulus | -0.2603367 | 0.1011099 | -0.5724773 | 0.0518040 |
| Eubacterium_rectale | -0.0129466 | 0.9645861 | -0.5900731 | 0.5641798 |
| Eubacterium_siraeum | -0.0140950 | 0.9710428 | -0.7825936 | 0.7544037 |
| Eubacterium_ventriosum | -0.1389631 | 0.6478496 | -0.7408047 | 0.4628784 |
| Faecalibacterium_SGB15346 | -0.2533722 | 0.2401229 | -0.6787848 | 0.1720405 |
| Faecalibacterium_prausnitzii | -0.2262934 | 0.1740079 | -0.5542123 | 0.1016256 |
| Faecalibacterium_sp_CLA_AA_H233 | -0.6906235 | 0.0215382 | -1.2773849 | -0.1038621 |
| Faecalibacterium_sp_HTFF | -0.4697997 | 0.1064197 | -1.0419248 | 0.1023254 |
| Faecalicatena_fissicatena | 0.0967373 | 0.7096708 | -0.4173568 | 0.6108313 |
| Flavonifractor_plautii | -0.2384383 | 0.4519574 | -0.8649620 | 0.3880853 |
| Fusicatenibacter_saccharivorans | 0.2304512 | 0.2259058 | -0.1447982 | 0.6057006 |
| Fusicatenibacter_sp_CLA_AA_H277 | 0.0242508 | 0.8934732 | -0.3341621 | 0.3826637 |
| GGB13404_SGB14252 | 0.2038157 | 0.3857088 | -0.2603452 | 0.6679765 |
| GGB1420_SGB1957 | -0.3330708 | 0.0511249 | -0.6678015 | 0.0016600 |
| GGB2653_SGB3574 | 0.0456495 | 0.8480939 | -0.4259832 | 0.5172822 |
| GGB2998_SGB3988 | -0.0336482 | 0.8763545 | -0.4616444 | 0.3943480 |
| GGB3034_SGB4030 | 0.6962316 | 0.0167594 | 0.1284732 | 1.2639899 |
| GGB3109_SGB4121 | -0.4282785 | 0.0133457 | -0.7655423 | -0.0910147 |
| GGB3175_SGB4191 | -0.5151292 | 0.0490286 | -1.0280226 | -0.0022359 |
| GGB33469_SGB15236 | 0.0547046 | 0.8410499 | -0.4851140 | 0.5945232 |
| GGB33512_SGB15203 | -0.3457539 | 0.2536613 | -0.9432656 | 0.2517579 |
| GGB33586_SGB53517 | 0.5332804 | 0.0751835 | -0.0551460 | 1.1217067 |
| GGB3537_SGB4727 | 0.1435250 | 0.6343154 | -0.4533352 | 0.7403852 |
| GGB38744_SGB14842 | 1.0430771 | 0.0015441 | 0.4075608 | 1.6785934 |
| GGB45432_SGB63101 | 0.2514547 | 0.3905059 | -0.3270381 | 0.8299474 |
| GGB45613_SGB63326 | 0.3088180 | 0.4541052 | -0.5065140 | 1.1241501 |
| GGB47687_SGB2286 | 0.0738015 | 0.6715738 | -0.2705524 | 0.4181554 |
| GGB52106_SGB72838 | 0.3734460 | 0.1885440 | -0.1862099 | 0.9331018 |
| GGB52130_SGB14966 | 0.6001682 | 0.0216521 | 0.0898028 | 1.1105335 |
| GGB9062_SGB13981 | 0.2870239 | 0.4246162 | -0.4233169 | 0.9973647 |
| GGB9063_SGB13982 | 0.1213392 | 0.6274187 | -0.3731619 | 0.6158403 |
| GGB9064_SGB13983 | -0.1060654 | 0.6944834 | -0.6403210 | 0.4281902 |
| GGB9342_SGB14306 | -0.1090269 | 0.6337649 | -0.5616879 | 0.3436340 |
| GGB9345_SGB14311 | -0.6261437 | 0.0136545 | -1.1209108 | -0.1313765 |
| GGB9453_SGB14844 | -0.1624281 | 0.3976526 | -0.5418189 | 0.2169627 |
| GGB9502_SGB14899 | -0.3142442 | 0.0637990 | -0.6468678 | 0.0183795 |
| GGB9509_SGB14906 | -0.2012361 | 0.3732921 | -0.6476902 | 0.2452180 |
| GGB9522_SGB14921 | -0.0856743 | 0.6497963 | -0.4589391 | 0.2875904 |
| GGB9531_SGB14932 | 0.0832237 | 0.7472669 | -0.4277969 | 0.5942442 |
| GGB9534_SGB14937 | 0.9503439 | 0.0020320 | 0.3554000 | 1.5452879 |
| GGB9602_SGB15031 | -0.2983810 | 0.2842465 | -0.8482758 | 0.2515138 |
| GGB9614_SGB15049 | -0.1057539 | 0.5933164 | -0.4974092 | 0.2859014 |
| GGB9619_SGB15067 | -0.0658281 | 0.8156820 | -0.6246809 | 0.4930247 |
| GGB9621_SGB15073 | 0.6829391 | 0.0332750 | 0.0552563 | 1.3106219 |
| GGB9635_SGB15106 | -0.7209995 | 0.0278304 | -1.3617952 | -0.0802037 |
| GGB9646_SGB15123 | 0.1659579 | 0.6161645 | -0.4888612 | 0.8207769 |
| GGB9667_SGB15164 | 0.1939356 | 0.4905662 | -0.3621603 | 0.7500315 |
| GGB9699_SGB15216 | -0.1154958 | 0.7079297 | -0.7254431 | 0.4944515 |
| GGB9708_SGB15234 | -0.3044069 | 0.2555122 | -0.8325325 | 0.2237187 |
| GGB9715_SGB15265 | -0.0395713 | 0.8828052 | -0.5708351 | 0.4916925 |
| GGB9719_SGB15272 | 0.0933414 | 0.7784423 | -0.5631568 | 0.7498397 |
| GGB9719_SGB15273 | 0.3419837 | 0.1182284 | -0.0885956 | 0.7725630 |
| GGB9730_SGB15291 | -0.3397912 | 0.0556582 | -0.6879557 | 0.0083733 |
| GGB9758_SGB15368 | 0.0479382 | 0.8890711 | -0.6322707 | 0.7281472 |
| GGB9760_SGB15373 | -0.2738247 | 0.1788212 | -0.6751025 | 0.1274531 |
| GGB9765_SGB15382 | 0.3559094 | 0.1954146 | -0.1858484 | 0.8976672 |
| GGB9770_SGB15390 | 0.2845921 | 0.2368495 | -0.1898957 | 0.7590799 |
| GGB9775_SGB15395 | -0.1485127 | 0.4852481 | -0.5691760 | 0.2721506 |
| GGB9781_SGB15402 | 0.5571759 | 0.0295710 | 0.0564116 | 1.0579401 |
| GGB9818_SGB15459 | -0.1679343 | 0.5833727 | -0.7734864 | 0.4376179 |
| Gemmiger_formicilis | -0.3194152 | 0.2837946 | -0.9075192 | 0.2686887 |
| Guopingia_tenuis | 0.3191492 | 0.4287082 | -0.4777396 | 1.1160380 |
| Holdemania_filiformis | 0.8843009 | 0.0014772 | 0.3478156 | 1.4207862 |
| Hydrogenoanaerobacterium_saccharovorans | -0.4185804 | 0.0049499 | -0.7074932 | -0.1296677 |
| Intestinimonas_butyriciproducens | 0.0089281 | 0.9803592 | -0.7088469 | 0.7267031 |
| Intestinimonas_gabonensis | -0.1831603 | 0.6305360 | -0.9364266 | 0.5701061 |
| Intestinimonas_massiliensis | 0.6341853 | 0.0285001 | 0.0680849 | 1.2002857 |
| Lachnoclostridium_sp_An138 | -0.0435669 | 0.8425183 | -0.4775438 | 0.3904100 |
| Lachnospira_eligens | 0.0924010 | 0.7642934 | -0.5173738 | 0.7021757 |
| Lachnospira_pectinoschiza | 0.0255369 | 0.9434809 | -0.6873761 | 0.7384499 |
| Lachnospiraceae_bacterium | -0.3042466 | 0.1525318 | -0.7229708 | 0.1144776 |
| Lachnospiraceae_bacterium_AM48_27BH | 0.0756174 | 0.6192999 | -0.2254218 | 0.3766565 |
| Lachnospiraceae_bacterium_CLA_AA_H215 | -0.3672498 | 0.1048809 | -0.8124932 | 0.0779937 |
| Lachnospiraceae_bacterium_CLA_AA_H244 | -0.2604068 | 0.2598342 | -0.7163438 | 0.1955301 |
| Lachnotalea_sp_AF33_28 | 0.5603215 | 0.1053793 | -0.1199840 | 1.2406270 |
| Lacrimispora_amygdalina | 0.2502885 | 0.2215733 | -0.1534390 | 0.6540161 |
| Lawsonibacter_SGB15145 | -0.4051988 | 0.0175845 | -0.7381619 | -0.0722358 |
| Lawsonibacter_asaccharolyticus | -0.8174813 | 0.0048166 | -1.3798964 | -0.2550663 |
| Lawsonibacter_hominis | -0.0136630 | 0.9671727 | -0.6707464 | 0.6434203 |
| Ligaoa_zhengdingensis | -0.1598639 | 0.6505451 | -0.8579574 | 0.5382297 |
| Mediterraneibacter_faecis | -1.4644428 | 0.0000000 | -1.8413197 | -1.0875658 |
| Odoribacter_splanchnicus | -0.6821452 | 0.0000286 | -0.9905626 | -0.3737278 |
| Oliverpabstia_intestinalis | -0.8044961 | 0.0000562 | -1.1836306 | -0.4253617 |
| Oscillibacter_sp_ER4 | -0.2381552 | 0.3320725 | -0.7229604 | 0.2466500 |
| Oscillibacter_sp_MSJ_31 | -0.4765347 | 0.0830886 | -1.0166200 | 0.0635506 |
| Oscillibacter_sp_PC13 | 0.7156796 | 0.0971098 | -0.1321697 | 1.5635290 |
| Oscillibacter_valericigenes | -0.0959740 | 0.7011394 | -0.5907381 | 0.3987902 |
| Oscillospiraceae_bacterium | -0.8911802 | 0.0023796 | -1.4581893 | -0.3241711 |
| Oscillospiraceae_bacterium_CLA_AA_H250 | -0.3197186 | 0.2250654 | -0.8393750 | 0.1999378 |
| Oscillospiraceae_bacterium_Marseille_Q3528 | -0.0646419 | 0.6990623 | -0.3954645 | 0.2661807 |
| Parabacteroides_distasonis | -0.3658317 | 0.0505524 | -0.7325608 | 0.0008974 |
| Parabacteroides_merdae | -0.2503076 | 0.2058630 | -0.6403422 | 0.1397270 |
| Paraprevotella_clara | -0.0364840 | 0.8481744 | -0.4136241 | 0.3406562 |
| Parasutterella_excrementihominis | 0.2896829 | 0.3987431 | -0.3885143 | 0.9678801 |
| Phascolarctobacterium_faecium | 0.0017026 | 0.9949541 | -0.5311556 | 0.5345608 |
| Phocaeicola_dorei | -0.2834248 | 0.3845410 | -0.9272939 | 0.3604443 |
| Phocaeicola_sartorii | 0.0000000 | NaN | 0.0000000 | 0.0000000 |
| Phocaeicola_vulgatus | -0.1565157 | 0.6106139 | -0.7644806 | 0.4514493 |
| Phocea_massiliensis | 0.0674568 | 0.8597579 | -0.6881407 | 0.8230542 |
| Provencibacterium_massiliense | 0.3298768 | 0.3869191 | -0.4232944 | 1.0830479 |
| Pseudoflavonifractor_capillosus | -0.0051894 | 0.9892089 | -0.7645954 | 0.7542166 |
| Roseburia_faecis | 0.4290783 | 0.2610326 | -0.3240827 | 1.1822392 |
| Roseburia_hominis | 1.2752450 | 0.0001261 | 0.6412974 | 1.9091926 |
| Roseburia_intestinalis | -0.6589740 | 0.0670335 | -1.3650660 | 0.0471180 |
| Roseburia_inulinivorans | -0.4382647 | 0.1540169 | -1.0436397 | 0.1671102 |
| Ruminococcus_bicirculans | -0.1796234 | 0.6298917 | -0.9169524 | 0.5577056 |
| Ruminococcus_bromii | -0.5545669 | 0.1901062 | -1.3886202 | 0.2794864 |
| Ruminococcus_torques | -0.3437329 | 0.2409635 | -0.9219013 | 0.2344355 |
| Ruthenibacterium_lactatiformans | 0.0673499 | 0.8131221 | -0.4964434 | 0.6311432 |
| Segatella_copri | -0.3326160 | 0.5795627 | -1.5199399 | 0.8547079 |
| Simiaoa_sunii | -0.8033900 | 0.0368014 | -1.5565334 | -0.0502465 |
| Streptococcus_salivarius | -0.9700788 | 0.0059191 | -1.6543357 | -0.2858219 |
| Streptococcus_thermophilus | -0.4850060 | 0.0969138 | -1.0592397 | 0.0892278 |
| Sutterella_wadsworthensis | -0.5994318 | 0.0097883 | -1.0509554 | -0.1479083 |
| Vescimonas_coprocola | -0.2536396 | 0.3344338 | -0.7725060 | 0.2652269 |
| Wansuia_hejianensis | 0.1636774 | 0.4748630 | -0.2890765 | 0.6164313 |
| Youxingia_wuxianensis | 0.9952571 | 0.0074120 | 0.2729631 | 1.7175511 |
| bacterium_210917_DFI_7_65 | 0.0132664 | 0.9490081 | -0.3973007 | 0.4238335 |
| Bacteroides_faecis | 0.1426993 | 0.4396300 | -0.2222049 | 0.5076035 |
| Clostridiaceae_unclassified_SGB4771 | 0.2898282 | 0.1623543 | -0.1186999 | 0.6983563 |
| Clostridium_sp_AM49_4BH | -0.1319839 | 0.6414443 | -0.6926274 | 0.4286595 |
| Colidextribacter_sp_210702_DFI_3_9 | -0.0469760 | 0.8580027 | -0.5665904 | 0.4726384 |
| Enterocloster_lavalensis | -0.1157850 | 0.6102710 | -0.5651044 | 0.3335345 |
| GGB2982_SGB3964 | -0.1414619 | 0.1574043 | -0.3384871 | 0.0555632 |
| GGB3304_SGB4367 | -0.2141347 | 0.3447208 | -0.6616619 | 0.2333925 |
| GGB3619_SGB4894 | -0.1425176 | 0.5727179 | -0.6421960 | 0.3571607 |
| GGB9296_SGB14253 | 0.1413539 | 0.4128722 | -0.1997268 | 0.4824345 |
| GGB9524_SGB14924 | -0.4280648 | 0.0233726 | -0.7968804 | -0.0592492 |
| GGB9574_SGB14987 | -0.6708302 | 0.0079814 | -1.1624111 | -0.1792493 |
| GGB9619_SGB15066 | 0.7867548 | 0.0027338 | 0.2788275 | 1.2946820 |
| GGB9707_SGB15229 | 0.1067650 | 0.6112393 | -0.3086787 | 0.5222086 |
| GGB9708_SGB15233 | 0.0740248 | 0.7873171 | -0.4689180 | 0.6169677 |
| GGB9760_SGB15374 | -0.0883561 | 0.6231081 | -0.4439741 | 0.2672618 |
| Roseburia_sp_AF02_12 | -0.7572841 | 0.0689237 | -1.5744006 | 0.0598324 |
| Segatella_brunsvicensis | -0.4376605 | 0.1411815 | -1.0231361 | 0.1478151 |
| Wujia_chipingensis | -0.3435443 | 0.2324910 | -0.9109729 | 0.2238842 |
| Alistipes_dispar | 0.1980443 | 0.2570647 | -0.1466802 | 0.5427688 |
| Alistipes_sp_AF17_16 | -0.0135480 | 0.9428643 | -0.3876781 | 0.3605821 |
| Anaerobutyricum_soehngenii | -0.2252784 | 0.5383520 | -0.9492191 | 0.4986624 |
| Anaerosacchariphilus_sp_NSJ_68 | 0.5567885 | 0.0518067 | -0.0044448 | 1.1180218 |
| Anaerotignum_sp_MSJ_24 | 0.3290706 | 0.1092091 | -0.0749030 | 0.7330441 |
| Bittarella_massiliensis | 1.0542704 | 0.0050189 | 0.3253885 | 1.7831524 |
| Blautia_SGB4815 | -1.0178179 | 0.0001166 | -1.5210841 | -0.5145517 |
| Blautia_luti | 0.0602180 | 0.7820664 | -0.3705466 | 0.4909826 |
| Blautia_sp_OF03_15BH | 0.0468998 | 0.8402839 | -0.4136520 | 0.5074517 |
| Butyricimonas_paravirosa | 0.6661290 | 0.0011973 | 0.2699331 | 1.0623250 |
| Catenibacillus_scindens | 0.8575408 | 0.0104144 | 0.2060001 | 1.5090815 |
| Clostridiaceae_bacterium_Marseille_Q4149 | -0.2451357 | 0.2656415 | -0.6796228 | 0.1893515 |
| Clostridium_SGB6173 | -0.1714187 | 0.6231528 | -0.8614376 | 0.5186003 |
| Clostridium_SGB6179 | -0.0567863 | 0.8481564 | -0.6437244 | 0.5301517 |
| Clostridium_sp_Marseille_P3244 | 0.0920410 | 0.8388431 | -0.8035997 | 0.9876817 |
| Clostridium_sp_NSJ_42 | 0.0610109 | 0.7988062 | -0.4126544 | 0.5346763 |
| Coprobacter_secundus | 0.8334583 | 0.0001341 | 0.4173651 | 1.2495515 |
| Eubacteriaceae_bacterium | -0.0459075 | 0.8802065 | -0.6487671 | 0.5569521 |
| Faecalibacillus_faecis | 0.2289766 | 0.3322933 | -0.2373579 | 0.6953112 |
| Faecalibacillus_intestinalis | 0.0074233 | 0.9763810 | -0.4888300 | 0.5036766 |
| GGB13489_SGB15224 | -0.1187886 | 0.6059785 | -0.5742734 | 0.3366962 |
| GGB2970_SGB3952 | 0.1460377 | 0.3704544 | -0.1760309 | 0.4681062 |
| GGB3352_SGB4436 | 0.5920488 | 0.0295483 | 0.0600183 | 1.1240793 |
| GGB34797_SGB14322 | -0.8256021 | 0.0001124 | -1.2327896 | -0.4184145 |
| GGB34900_SGB14891 | 0.7211672 | 0.0382694 | 0.0397665 | 1.4025679 |
| GGB3653_SGB4964 | 0.0655478 | 0.8033933 | -0.4554745 | 0.5865700 |
| GGB4456_SGB6141 | 0.2806543 | 0.2430794 | -0.1935551 | 0.7548637 |
| GGB4552_SGB6276 | 0.0736109 | 0.7693499 | -0.4231396 | 0.5703614 |
| GGB51441_SGB71759 | 0.2405052 | 0.2167575 | -0.1433775 | 0.6243878 |
| GGB58158_SGB79798 | 0.5889548 | 0.1781303 | -0.2727474 | 1.4506571 |
| GGB9365_SGB14341 | -0.0567238 | 0.8336735 | -0.5912952 | 0.4778475 |
| GGB9412_SGB14770 | 0.5980316 | 0.0018600 | 0.2269535 | 0.9691097 |
| GGB9627_SGB15081 | 0.2596162 | 0.2650512 | -0.1999651 | 0.7191975 |
| GGB9712_SGB15244 | -0.2739057 | 0.0943491 | -0.5956694 | 0.0478579 |
| GGB9747_SGB15356 | -0.4817909 | 0.0318036 | -0.9207757 | -0.0428060 |
| GGB9767_SGB15385 | 0.4391785 | 0.0151973 | 0.0864618 | 0.7918952 |
| GGB9787_SGB15410 | 0.6099757 | 0.0062157 | 0.1771002 | 1.0428511 |
| GGB9790_SGB15413 | -0.0550261 | 0.7687885 | -0.4254316 | 0.3153795 |
| Haemophilus_parainfluenzae | 0.2149287 | 0.4472719 | -0.3439962 | 0.7738537 |
| Intestinibacter_bartlettii | -0.7170859 | 0.0142129 | -1.2871425 | -0.1470294 |
| Lachnospira_sp_NSJ_43 | 0.6837830 | 0.0050380 | 0.2108276 | 1.1567383 |
| Lachnospiraceae_bacterium_OM04_12BH | 0.2308796 | 0.4846970 | -0.4222615 | 0.8840206 |
| Lactococcus_lactis | 1.0243734 | 0.0001764 | 0.5029699 | 1.5457770 |
| Lentihominibacter_faecis | 0.4104142 | 0.0613862 | -0.0199581 | 0.8407866 |
| Massilioclostridium_coli | 0.7560415 | 0.0677404 | -0.0561873 | 1.5682702 |
| Mediterraneibacter_butyricigenes | 0.2926664 | 0.1789369 | -0.1363383 | 0.7216712 |
| Mediterraneibacter_sp_NSJ_151 | -0.0661280 | 0.7868718 | -0.5501119 | 0.4178559 |
| Methanobrevibacter_smithii | -0.1398588 | 0.6387379 | -0.7291598 | 0.4494422 |
| Romboutsia_timonensis | -0.4420490 | 0.2203266 | -1.1531583 | 0.2690602 |
| Ruminococcus_gnavus | -0.2896922 | 0.2618347 | -0.7990501 | 0.2196657 |
| Ruminococcus_lactaris | -0.5709585 | 0.0153996 | -1.0304470 | -0.1114699 |
| Ruminococcus_sp_AF41_9 | 0.3716328 | 0.0953338 | -0.0662553 | 0.8095209 |
| Senegalimassilia_anaerobia | -0.2760952 | 0.0044868 | -0.4644656 | -0.0877247 |
| Slackia_isoflavoniconvertens | -0.3934137 | 0.0092664 | -0.6875335 | -0.0992939 |
| Streptococcus_parasanguinis | -0.3339438 | 0.2667054 | -0.9271643 | 0.2592768 |
| Veillonella_dispar | 0.1429699 | 0.6546016 | -0.4892106 | 0.7751504 |
| Victivallis_lenta | 0.2228559 | 0.3279291 | -0.2269162 | 0.6726281 |
| Bifidobacterium_pseudocatenulatum | 0.1556873 | 0.6136983 | -0.4543332 | 0.7657078 |
| Eubacterium_sp_AF34_35BH | 0.2268773 | 0.2467866 | -0.1595118 | 0.6132664 |
| Faecalicatena_contorta | -0.6498984 | 0.0681419 | -1.3491323 | 0.0493355 |
| GGB9559_SGB14969 | 0.2890652 | 0.1298004 | -0.0864046 | 0.6645350 |
| GGB9759_SGB15370 | 0.2873475 | 0.1206768 | -0.0768754 | 0.6515704 |
| Roseburia_lenta | 0.2487548 | 0.2102571 | -0.1426542 | 0.6401638 |
| Enterocloster_bolteae | -0.2708939 | 0.4398033 | -0.9638748 | 0.4220870 |
| GGB2848_SGB3813 | -0.2851155 | 0.2844685 | -0.8108065 | 0.2405756 |
| GGB3005_SGB3996 | 0.1700297 | 0.4494938 | -0.2743112 | 0.6143706 |
| GGB3061_SGB4063 | 0.2825993 | 0.2147087 | -0.1664476 | 0.7316462 |
| GGB36331_SGB15121 | -0.2099425 | 0.0563573 | -0.4256832 | 0.0057981 |
| Hungatella_hathewayi | -0.3753375 | 0.0883542 | -0.8080524 | 0.0573775 |
| TM7_phylum_sp_oral_taxon_352 | 0.2849872 | 0.3473720 | -0.3139150 | 0.8838894 |
| Veillonella_parvula | 0.6430477 | 0.0321454 | 0.0559377 | 1.2301577 |
| GGB6649_SGB9391 | 0.0682979 | 0.7049816 | -0.2886098 | 0.4252055 |
| Veillonella_atypica | -0.0713555 | 0.8322438 | -0.7379991 | 0.5952881 |
Open code
if (file.exists("gitignore/result_microbiom_validation.csv") == FALSE) {
write.table(result_microbiome_val,
"gitignore/result_microbiom_validation.csv",
row.names = FALSE
)
}6.2.2 Forest plot
6.2.2.1 Prepare data
Open code
## relevant microbiome
diet_sensitive_microbiome <- result_microbiome %>%
filter(
fdr_VGdiet_avg < 0.1,
outcome %in% common_microbiome
) %>%
select(
outcome
)
len <- nrow(diet_sensitive_microbiome)
## subset result tables
result_microbiome_subset <- result_microbiome %>%
filter(outcome %in% diet_sensitive_microbiome$outcome,
outcome %in% common_microbiome)
result_microbiome_val_subset <- result_microbiome_val %>%
filter(outcome %in% diet_sensitive_microbiome$outcome,
outcome %in% common_microbiome)
## create a data frame
data_forest <- data.frame(
outcome = rep(diet_sensitive_microbiome$outcome, 3),
beta = c(
result_microbiome_subset$logFD_VGdiet_inCZ,
result_microbiome_subset$logFD_VGdiet_inIT,
result_microbiome_val_subset$logFD_VGdiet
),
lower = c(
result_microbiome_subset$CI_L_VGdiet_inCZ,
result_microbiome_subset$CI_L_VGdiet_inIT,
result_microbiome_val_subset$CI_L_VGdiet
),
upper = c(
result_microbiome_subset$CI_U_VGdiet_inCZ,
result_microbiome_subset$CI_U_VGdiet_inIT,
result_microbiome_val_subset$CI_U_VGdiet
),
dataset = c(
rep("CZ", len),
rep("IT", len),
rep("Validation", len)
)
)6.2.2.2 Create forest plot
Open code
colors <- c("CZ" = "#150999", "IT" = "#329243", "Validation" = "grey60")
# Create the forest plot
ggplot(data_forest, aes(x = outcome, y = beta, ymin = lower, ymax = upper, color = dataset)) +
geom_pointrange(position = position_dodge(width = 0.5), size = 0.5) +
geom_hline(yintercept = 0, color = 'black') +
geom_errorbar(position = position_dodge(width = 0.5), width = 0.2) +
scale_color_manual(values = colors) +
labs(
y = "Effect of vegan diet on log2-trasformed microbiome level",
x = "Outcome",
color = "Dataset"
) +
theme_minimal() +
coord_flip() + # Flip coordinates to have outcomes on the y-axis
theme(
axis.text.x = element_text(size = 10),
axis.text.y = element_text(size = 10),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
legend.position = "bottom"
) 
Diet, Country, and the interaction term Diet:Country as predictors. In the independent Czech validation cohort, Diet was the only fixed-effect predictor7 Reproducibility
Open code
sessionInfo()
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=cs_CZ.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=cs_CZ.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Europe/Prague
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MicrobiomeStat_1.2 glmnet_4.1-8 pROC_1.18.0 arm_1.12-2
## [5] lme4_1.1-35.5 Matrix_1.7-0 MASS_7.3-61 car_3.1-2
## [9] carData_3.0-5 emmeans_1.10.4 brms_2.21.0 Rcpp_1.0.13
## [13] rms_6.8-1 Hmisc_5.1-3 glmmTMB_1.1.9 ggdist_3.3.2
## [17] cowplot_1.1.1 ggpubr_0.4.0 sjPlot_2.8.16 kableExtra_1.4.0
## [21] flextable_0.9.6 gtsummary_2.0.2 compositions_2.0-8 janitor_2.2.0
## [25] stringi_1.7.6 lubridate_1.8.0 forcats_1.0.0 stringr_1.5.1
## [29] dplyr_1.1.4 purrr_1.0.2 readr_2.1.2 tidyr_1.3.1
## [33] tibble_3.2.1 ggplot2_3.5.1 tidyverse_1.3.1 readxl_1.3.1
## [37] openxlsx_4.2.5 RJDBC_0.2-10 rJava_1.0-6 DBI_1.1.2
##
## loaded via a namespace (and not attached):
## [1] fs_1.6.4 matrixStats_1.3.0 httr_1.4.2
## [4] insight_0.20.2 numDeriv_2016.8-1.1 tools_4.4.2
## [7] backports_1.5.0 sjlabelled_1.2.0 utf8_1.2.4
## [10] R6_2.5.1 mgcv_1.9-1 withr_3.0.1
## [13] Brobdingnag_1.2-7 prettyunits_1.1.1 gridExtra_2.3
## [16] bayesm_3.1-6 quantreg_5.98 cli_3.6.3
## [19] textshaping_0.3.6 performance_0.12.2 officer_0.6.6
## [22] sandwich_3.0-1 labeling_0.4.2 mvtnorm_1.1-3
## [25] robustbase_0.93-9 polspline_1.1.25 ggridges_0.5.3
## [28] askpass_1.1 QuickJSR_1.3.1 systemfonts_1.0.4
## [31] StanHeaders_2.32.10 foreign_0.8-86 gfonts_0.2.0
## [34] svglite_2.1.0 rstudioapi_0.16.0 httpcode_0.3.0
## [37] generics_0.1.3 shape_1.4.6 distributional_0.4.0
## [40] zip_2.2.0 inline_0.3.19 loo_2.4.1
## [43] fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4
## [46] multcomp_1.4-18 yaml_2.3.5 snakecase_0.11.1
## [49] grid_4.4.2 promises_1.2.0.1 crayon_1.5.0
## [52] lattice_0.22-5 haven_2.4.3 pillar_1.9.0
## [55] knitr_1.48 statip_0.2.3 boot_1.3-30
## [58] estimability_1.5.1 codetools_0.2-19 glue_1.7.0
## [61] V8_4.4.2 fontLiberation_0.1.0 data.table_1.15.4
## [64] vctrs_0.6.5 cellranger_1.1.0 gtable_0.3.0
## [67] assertthat_0.2.1 datawizard_0.12.2 xfun_0.46
## [70] mime_0.12 coda_0.19-4 modeest_2.4.0
## [73] survival_3.7-0 timeDate_3043.102 iterators_1.0.14
## [76] statmod_1.4.36 ellipsis_0.3.2 TH.data_1.1-0
## [79] nlme_3.1-165 fontquiver_0.2.1 rstan_2.32.6
## [82] fBasics_4041.97 tensorA_0.36.2.1 TMB_1.9.14
## [85] rpart_4.1.23 colorspace_2.0-2 nnet_7.3-19
## [88] tidyselect_1.2.1 processx_3.8.4 timeSeries_4032.109
## [91] compiler_4.4.2 curl_4.3.2 rvest_1.0.2
## [94] htmlTable_2.4.0 SparseM_1.81 xml2_1.3.3
## [97] fontBitstreamVera_0.1.1 posterior_1.6.0 checkmate_2.3.2
## [100] scales_1.3.0 DEoptimR_1.0-10 callr_3.7.6
## [103] spatial_7.3-15 digest_0.6.37 minqa_1.2.4
## [106] rmarkdown_2.27 htmltools_0.5.8.1 pkgconfig_2.0.3
## [109] base64enc_0.1-3 stabledist_0.7-2 dbplyr_2.1.1
## [112] fastmap_1.2.0 rlang_1.1.4 htmlwidgets_1.6.4
## [115] shiny_1.9.1 farver_2.1.0 zoo_1.8-9
## [118] jsonlite_1.8.8 magrittr_2.0.3 Formula_1.2-4
## [121] bayesplot_1.8.1 munsell_0.5.0 gdtools_0.3.7
## [124] stable_1.1.6 plyr_1.8.6 pkgbuild_1.3.1
## [127] parallel_4.4.2 ggrepel_0.9.5 sjmisc_2.8.10
## [130] ggeffects_1.7.0 splines_4.4.2 hms_1.1.1
## [133] sjstats_0.19.0 ps_1.7.7 uuid_1.0-3
## [136] ggsignif_0.6.3 stats4_4.4.2 rmutil_1.1.10
## [139] rstantools_2.1.1 crul_1.5.0 reprex_2.0.1
## [142] evaluate_1.0.0 RcppParallel_5.1.8 modelr_0.1.8
## [145] nloptr_2.0.0 tzdb_0.2.0 foreach_1.5.2
## [148] httpuv_1.6.5 MatrixModels_0.5-3 openssl_1.4.6
## [151] clue_0.3-65 broom_1.0.6 xtable_1.8-4
## [154] rstatix_0.7.0 later_1.3.0 viridisLite_0.4.0
## [157] ragg_1.2.1 lmerTest_3.1-3 cluster_2.1.6
## [160] bridgesampling_1.1-2References
Lenth, Russell V. 2024. “Emmeans: Estimated Marginal Means, Aka Least-Squares Means.” https://CRAN.R-project.org/package=emmeans.